From 243606c5cbf7f27698b6f9578069a5c226eac7d4 Mon Sep 17 00:00:00 2001 From: Lukas Wallrich Date: Sun, 22 Mar 2026 22:24:01 +0000 Subject: [PATCH 01/11] Add data-driven Clusters v4.1 page with 11 clusters from Google Sheet Replace the 7 hardcoded cluster markdown files with a data-driven approach that reads from a generated JSON file (clusters_v4.json). The data originates from the FORRT Clusters v4.1 Google Doc and is parsed into a Google Sheet, then exported as JSON for Hugo to consume at build time. Key changes: - New script (parse_clusters_to_sheet.py) that parses the GDoc, resolves DOIs via doi.org for clean APA references + BibTeX, writes to Google Sheet, and exports JSON for Hugo - New Hugo shortcode (clusters_display.html) renders all clusters with sidebar navigation, tabbed sub-clusters, and full-text search - Updated intro text to reflect 11 clusters (was 9) - Deactivated old cluster1-7.md files (replaced by data-driven rendering) Co-Authored-By: Claude Opus 4.6 (1M context) --- .gitignore | 3 + assets/scss/custom.scss | 337 + content/clusters/cluster1.md | 2 +- content/clusters/cluster2.md | 2 +- content/clusters/cluster3.md | 2 +- content/clusters/cluster4.md | 2 +- content/clusters/cluster5.md | 2 +- content/clusters/cluster6.md | 2 +- content/clusters/cluster7.md | 2 +- content/clusters/clusters-data.md | 21 + content/clusters/intro-clusters.md | 8 +- data/clusters_v4.json | 7279 ++++++++++++++++++++++ layouts/shortcodes/clusters_display.html | 367 ++ scripts/parse_clusters_to_sheet.py | 1126 ++++ 14 files changed, 9145 insertions(+), 10 deletions(-) create mode 100644 content/clusters/clusters-data.md create mode 100644 data/clusters_v4.json create mode 100644 layouts/shortcodes/clusters_display.html create mode 100644 scripts/parse_clusters_to_sheet.py diff --git a/.gitignore b/.gitignore index 71e81880320..1316eb5401f 100644 --- a/.gitignore +++ b/.gitignore @@ -271,3 +271,6 @@ scripts/forrt_contribs/tenzing_failures.json # Bibtex to APA converter output bibtex_to_apa/node_modules/ + +# DOI lookup cache for cluster parsing script +scripts/doi_cache.json diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index 6f354b85885..4cc2c5d8dcb 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -28,6 +28,343 @@ } } +/* -------------------------------------------------- */ +/* Clusters v4 page styles */ +/* -------------------------------------------------- */ + +.clusters-layout { + margin-top: 0.5rem; +} + +/* ---- Mobile nav toggle ---- */ +.clusters-mobile-toggle { + width: 100%; + text-align: left; + font-size: 0.9rem; + padding: 0.5rem 1rem; + border-radius: 6px; +} + +.clusters-mobile-toggle.active { + background: #333; + color: #fff; + border-color: #333; +} + +/* ---- Sidebar ---- */ +.clusters-sidebar { + display: none; +} + +@media (min-width: 1200px) { + .clusters-sidebar { + display: block; + } +} + +.clusters-sidebar.sidebar-open { + display: block; +} + +.clusters-sidebar-inner { + position: sticky; + top: 60px; + max-height: calc(100vh - 80px); + overflow-y: auto; + padding: 0.75rem; + background: #f8f9fa; + border: 1px solid #e9ecef; + border-radius: 8px; + font-size: 0.82rem; +} + +.sidebar-header { + font-size: 0.75rem; + font-weight: 700; + text-transform: uppercase; + letter-spacing: 0.5px; + color: #888; + margin-bottom: 0.5rem; +} + +.cluster-nav-heading { + display: flex; + align-items: center; + gap: 0.3rem; + padding: 0.35rem 0.25rem; + font-weight: 600; + color: #333; + text-decoration: none !important; + font-size: 0.82rem; + cursor: pointer; + border-radius: 4px; + line-height: 1.3; +} + +.cluster-nav-heading:hover { + background: rgba(0,0,0,0.04); + color: #111; +} + +.cluster-nav-toggle { + display: inline-block; + width: 1em; + flex-shrink: 0; + font-size: 0.9em; + transition: transform 0.15s; +} + +.cluster-nav-subs { + list-style: none; + padding-left: 1.6rem; + margin: 0 0 0.25rem 0; +} + +.cluster-nav-subs .nav-link { + padding: 0.2rem 0.35rem; + font-size: 0.78rem; + color: #555; + display: flex; + justify-content: space-between; + align-items: baseline; + gap: 0.5rem; + line-height: 1.3; + border-radius: 3px; +} + +.cluster-nav-subs .nav-link:hover { + background: rgba(0,0,0,0.04); + color: #111; + text-decoration: none; +} + +.cluster-nav-subs .badge { + font-size: 0.6rem; + font-weight: 400; + color: #999; + background: transparent; + flex-shrink: 0; +} + +/* ---- Cluster sections ---- */ +.cluster-section { + padding: 1.5rem 1.25rem; + margin-bottom: 0.75rem; + border-radius: 8px; + border: 1px solid rgba(0,0,0,0.06); +} + +.cluster-header { + margin-bottom: 0.5rem; +} + +.cluster-title { + font-size: 1.15rem; + font-weight: 700; + margin-bottom: 0.1rem; + display: flex; + align-items: center; + gap: 0.4rem; +} + +.cluster-number { + display: inline-flex; + align-items: center; + justify-content: center; + width: 1.6em; + height: 1.6em; + border-radius: 50%; + background: rgba(0,0,0,0.1); + font-size: 0.8em; + flex-shrink: 0; +} + +.cluster-stats { + font-size: 0.7rem; + color: #888; +} + +.cluster-description { + font-size: 0.8rem; + line-height: 1.5; + color: #555; + margin-bottom: 0.75rem; +} + +/* ---- Search bar ---- */ +.clusters-search-bar .form-control { + font-size: 0.9rem; + padding: 0.5rem 0.75rem; + border-radius: 6px; +} + +.cluster-search-results { + max-height: 350px; + overflow-y: auto; + background: #fff; + border: 1px solid #ddd; + border-radius: 6px; + margin-top: 0.25rem; +} + +.search-count { + font-size: 0.72rem; + color: #888; + padding: 0.4rem 0.75rem; + border-bottom: 1px solid #eee; +} + +.search-result-item { + display: block; + padding: 0.5rem 0.75rem; + border-bottom: 1px solid #f0f0f0; + color: #333; + text-decoration: none; + font-size: 0.8rem; +} + +.search-result-item:hover { + background: #f5f7fa; + text-decoration: none; + color: #111; +} + +.search-result-context { + display: block; + font-size: 0.7rem; + color: #888; + margin-bottom: 0.15rem; +} + +.search-snippet { + font-size: 0.78rem; + color: #444; +} + +.search-snippet mark { + background: #fff3cd; + padding: 0 0.1em; +} + +.search-no-results, .search-more { + padding: 0.5rem 0.75rem; + font-size: 0.78rem; + color: #888; +} + +/* ---- Sub-cluster tabs (styled like real tabs) ---- */ +.cluster-tabs { + flex-wrap: wrap; + margin-bottom: 0; + border-bottom: 1px solid rgba(0,0,0,0.15); +} + +.cluster-tabs .nav-item { + flex-shrink: 0; + max-width: 100%; +} + +.cluster-tabs .nav-link { + font-size: 0.78rem; + padding: 0.4rem 0.75rem; + color: #8b0000; + border: 1px solid transparent; + border-bottom: none; + margin-bottom: -1px; + white-space: normal; + word-break: break-word; + border-radius: 4px 4px 0 0; + transition: background 0.15s, color 0.15s; +} + +.cluster-tabs .nav-link:hover { + color: #5a0000; + background: rgba(255,255,255,0.5); +} + +.cluster-tabs .nav-link.active { + color: #000; + font-weight: 600; + background: rgba(255,255,255,0.7); + border-color: rgba(0,0,0,0.15); +} + +.tab-count { + font-size: 0.6rem; + color: #aaa; + margin-left: 0.15em; + font-weight: 400; +} + +.cluster-tab-content { + padding: 1.25rem 0.5rem; +} + +/* ---- Sub-cluster heading & description ---- */ +.sc-heading { + font-size: 1.1rem; + font-weight: 700; + margin-bottom: 0.5rem; +} + +.sc-description { + font-size: 0.85rem; + color: #444; + font-style: italic; + margin-bottom: 1rem; + line-height: 1.5; +} + +/* ---- Publication list ---- */ +.publication-list { + padding-left: 1.5rem; + margin: 0; +} + +.publication-item { + padding: 0.35rem 0; + font-size: 0.82rem; + line-height: 1.5; + margin-bottom: 0.3rem; +} + +.publication-item a { + color: #1c7ed6; + word-break: break-all; +} + +.publication-item a:hover { + color: #1264ab; +} + +/* ---- Responsive ---- */ +@media (max-width: 1199px) { + .clusters-sidebar-inner { + position: static; + max-height: 50vh; + margin-bottom: 1rem; + } + + .cluster-section { + padding: 1rem 0.75rem; + } + + .cluster-tabs .nav-link { + font-size: 0.68rem; + padding: 0.3rem 0.45rem; + } +} + +@media (max-width: 576px) { + .cluster-title { + font-size: 1rem; + } + + .publication-item { + font-size: 0.72rem; + } +} + // Widen article container for pages with tables to avoid horizontal scrolling // Note: :has() selector has 93%+ browser support as of 2025. Older browsers // will gracefully degrade to the original behavior with horizontal scrolling. diff --git a/content/clusters/cluster1.md b/content/clusters/cluster1.md index c6676f055ed..034f78586d1 100644 --- a/content/clusters/cluster1.md +++ b/content/clusters/cluster1.md @@ -5,7 +5,7 @@ widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 10 # Order that this section will appear. title = "Cluster 1: Reproducibility Crisis and Credibility Revolution" diff --git a/content/clusters/cluster2.md b/content/clusters/cluster2.md index 360ffc688af..21c7a9e994f 100644 --- a/content/clusters/cluster2.md +++ b/content/clusters/cluster2.md @@ -5,7 +5,7 @@ widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 10 # Order that this section will appear. title = "Cluster 2: Conceptual and Statistical Knowledge" diff --git a/content/clusters/cluster3.md b/content/clusters/cluster3.md index fb6cb9a5c86..9412065d520 100644 --- a/content/clusters/cluster3.md +++ b/content/clusters/cluster3.md @@ -5,7 +5,7 @@ widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 10 # Order that this section will appear. title = "Cluster 3: Reproducible analyses" diff --git a/content/clusters/cluster4.md b/content/clusters/cluster4.md index 9230fd6884d..3d351c07d30 100644 --- a/content/clusters/cluster4.md +++ b/content/clusters/cluster4.md @@ -5,7 +5,7 @@ widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 10 # Order that this section will appear. title = "Cluster 4: Open (FAIR) data and materials analyses" diff --git a/content/clusters/cluster5.md b/content/clusters/cluster5.md index 0dbbf32cfa5..08613f0bdca 100644 --- a/content/clusters/cluster5.md +++ b/content/clusters/cluster5.md @@ -5,7 +5,7 @@ widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 10 # Order that this section will appear. title = "Cluster 5: Preregistration" diff --git a/content/clusters/cluster6.md b/content/clusters/cluster6.md index f9c929b7d01..9af37db12ae 100644 --- a/content/clusters/cluster6.md +++ b/content/clusters/cluster6.md @@ -5,7 +5,7 @@ widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 10 # Order that this section will appear. title = "Cluster 6: Replication research" diff --git a/content/clusters/cluster7.md b/content/clusters/cluster7.md index 5291bbd0592..8d179217df3 100644 --- a/content/clusters/cluster7.md +++ b/content/clusters/cluster7.md @@ -5,7 +5,7 @@ widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ headless = true # This file represents a page section. -active = true # Activate this widget? true/false +active = false # Activate this widget? true/false weight = 10 # Order that this section will appear. title = "Cluster 7: Academic Life, Ethics and Culture" diff --git a/content/clusters/clusters-data.md b/content/clusters/clusters-data.md new file mode 100644 index 00000000000..68c897e1dd4 --- /dev/null +++ b/content/clusters/clusters-data.md @@ -0,0 +1,21 @@ ++++ +widget = "blank" +headless = true +active = true +weight = 10 + +title = "" +subtitle = "" + +[design] + columns = "1" + +[design.spacing] + padding = ["20px", "0", "60px", "0"] + +[advanced] + css_style = "" + css_class = "" ++++ + +{{< clusters_display >}} diff --git a/content/clusters/intro-clusters.md b/content/clusters/intro-clusters.md index c0b0347f6d3..91c322dda59 100644 --- a/content/clusters/intro-clusters.md +++ b/content/clusters/intro-clusters.md @@ -55,7 +55,7 @@ subtitle = ""
-In order to teach Open and Reproducible Science effectively, educators need to make sense of almost a decade of literature, across several fields, and be informed about ongoing (and often dynamic) debates. This is a tall ask for most educators. So FORRT sought to develop strategies and propose solutions to mitigate the effects of competing academic interests and help scholars implement open and reproducible science tenets in their teaching and mentoring workflow. In an effort to reduce some of the burden on educators wishing to learn or teach these concepts, FORRT has drawn on the expertise of more than 50 experts from its community to provide educators with a comprehensive but straightforward accessible didactic framework. FORRT clusters is a result of a comprehensive literature review guided by educational, pedagogical, and didactic considerations aiming at providing a pathway towards the incremental adoption of Open and Reproducible Science tenets into educators/scholars' teaching and mentoring. The focus lies not on simply aggregating the literature into bins, but on making sense of existing works, weaving connections where none exist, and providing a sensible learning-oriented Open and Reproducible Science taxonomy. FORRT taxonomy is composed of 9 clusters: +In order to teach Open and Reproducible Science effectively, educators need to make sense of almost a decade of literature, across several fields, and be informed about ongoing (and often dynamic) debates. This is a tall ask for most educators. So FORRT sought to develop strategies and propose solutions to mitigate the effects of competing academic interests and help scholars implement open and reproducible science tenets in their teaching and mentoring workflow. In an effort to reduce some of the burden on educators wishing to learn or teach these concepts, FORRT has drawn on the expertise of more than 50 experts from its community to provide educators with a comprehensive but straightforward accessible didactic framework. FORRT clusters is a result of a comprehensive literature review guided by educational, pedagogical and didactic considerations aiming at providing a pathway towards the incremental adoption of Open and Reproducible Science tenets into educators/scholars teaching and mentoring. The focus lies not on simply aggregating the literature into bins, but on making sense of existing works, weaving connections where none exist, and providing a sensible learning-oriented Open and Reproducible Science taxonomy. FORRT taxonomy is composed of 11 clusters: 1. Replicability crisis and credibility revolution knowledge 2. Conceptual and statistical knowledge @@ -66,10 +66,12 @@ In order to teach Open and Reproducible Science effectively, educators need to m 7. Publication sharing 8. Replication and meta-research 9. Academic structures and institutions +10. Qualitative Research +11. Research Integrity -These clusters contain information for quantitative and qualitative researchers. There is additionally an addendum which groups together the information provided for qualitative research. +These clusters contain information for quantitative and qualitative researchers. -We further break down each cluster into sub-categories to provide educators/scholars with useful information on the extent of open scholarship, and how they are connected to one another. The idea behind specifying clusters and sub-clusters is to highlight that we have drawn fuzzy boundaries between clusters, while allowing for diversification and heterogeneity in how each educator integrates these clusters/sub-clusters with their respective field content. The breakdown of each cluster into sub-categories provides scholars with useful information on the extent of open science scholarship, and how they are connected to one another. To have a look at the sub-clusters within each cluster, please click on the clusters above. +We further break down each cluster into sub-categories to provide educators/scholars with useful information on the extent of open scholarship, and how they are connected to one another. The idea behind specifying clusters and sub-clusters is to highlight that we have drawn fuzzy boundaries between clusters, while allowing for diversification and heterogeneity in how each educator integrates these cluster/sub-clusters with their respective field content. The breakdown of each cluster into sub-categories provides scholars with useful information on the extent of open science scholarship, and how they are connected to one another. See below for each cluster, its description, sub-clusters, and associated works geared for teaching. And here's an attempt to visualize FORRT's clusters: diff --git a/data/clusters_v4.json b/data/clusters_v4.json new file mode 100644 index 00000000000..000c85d377b --- /dev/null +++ b/data/clusters_v4.json @@ -0,0 +1,7279 @@ +{ + "clusters": [ + { + "number": 1, + "name": "Replication Crisis and Credibility Revolution", + "description": "Attainment of foundational knowledge on the importance of reproducible and open research (i.e., grounding the motivations and theoretical underpinnings of Open and Reproducible Science). Integration with field specific content (i.e., grounded in the history of replicability). There are 7 sub-clusters which aim to further parse the learning and teaching process:", + "sub_clusters": [ + { + "name": "History of the replication crisis & credibility revolution", + "description": "In order to understand and weigh in on current developments, we need to first understand how the Open and Reproducible Science movement started, from its origins over the replicability/reproducibility crisis to the credibility revolution.", + "publications": [ + { + "doi": "10.1177/09593543241250079", + "apa": "Archer, R. (2024). Retiring Popper: Critical realism, falsificationism, and the crisis of replication. Theory & Psychology, 34(5), 561–584. https://doi.org/10.1177/09593543241250079", + "auto_ref": true + }, + { + "doi": "10.1086/734279", + "apa": "Arel-Bundock, V., Briggs, R. C., Doucouliagos, H., Aviña, M. M., & Stanley, T. D. (2026). Quantitative Political Science Research Is Greatly Underpowered. The Journal of Politics, 88(1), 36–46. https://doi.org/10.1086/734279", + "auto_ref": true + }, + { + "doi": "10.1038/533452a", + "apa": "Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533(7604), 452–454. https://doi.org/10.1038/533452a", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-019-00067-3", + "apa": "Stoddart, C. (2016). Is there a reproducibility crisis in science? Nature. https://doi.org/10.1038/d41586-019-00067-3", + "auto_ref": true + }, + { + "doi": "10.1093/bjps/axy051", + "apa": "Bird, A. (2021). Understanding the Replication Crisis as a Base Rate Fallacy. The British Journal for the Philosophy of Science, 72(4), 965–993. https://doi.org/10.1093/bjps/axy051", + "auto_ref": true + }, + { + "doi": "10.1515/9781400884940", + "apa": "Chambers, C. (2017). The Seven Deadly Sins of Psychology. https://doi.org/10.1515/9781400884940", + "auto_ref": true + }, + { + "doi": "10.1007/s13164-018-0400-9", + "apa": "Cova, F., Strickland, B., Abatista, A., Allard, A., Andow, J., Attie, M., Beebe, J., Berniūnas, R., Boudesseul, J., Colombo, M., Cushman, F., Diaz, R., N’Djaye Nikolai van Dongen, N., Dranseika, V., Earp, B. D., Torres, A. G., Hannikainen, I., Hernández-Conde, J. V., Hu, W., … Zhou, X. (2018). Estimating the Reproducibility of Experimental Philosophy. Review of Philosophy and Psychology, 12(1), 9–44. https://doi.org/10.1007/s13164-018-0400-9", + "auto_ref": true + }, + { + "doi": "10.1027/2151-2604/a000387", + "apa": "Crüwell, S., van Doorn, J., Etz, A., Makel, M. C., Moshontz, H., Niebaum, J. C., Orben, A., Parsons, S., & Schulte-Mecklenbeck, M. (2019). Seven Easy Steps to Open Science. Zeitschrift Für Psychologie, 227(4), 237–248. https://doi.org/10.1027/2151-2604/a000387", + "auto_ref": true + }, + { + "doi": "10.1089/ees.2016.0223", + "apa": "Edwards, M. A., & Roy, S. (2017). Academic Research in the 21st Century: Maintaining Scientific Integrity in a Climate of Perverse Incentives and Hypercompetition. Environmental Engineering Science, 34(1), 51–61. https://doi.org/10.1089/ees.2016.0223", + "auto_ref": true + }, + { + "doi": "10.1017/psa.2024.2", + "apa": "Feest, U. (2024). What is the Replication Crisis a Crisis Of? Philosophy of Science, 91(5), 1361–1371. https://doi.org/10.1017/psa.2024.2", + "auto_ref": true + }, + { + "doi": "10.31222/osf.io/k5su6_v1", + "apa": "Haven, T. L., & Ioannidis, J. P. A. (2025). Reproducibility Failure in Biomedical Research: Problems and Solutions. https://doi.org/10.31222/osf.io/k5su6_v1", + "auto_ref": true + }, + { + "doi": "10.1038/s44271-023-00003-2", + "apa": "Korbmacher, M., Azevedo, F., Pennington, C. R., Hartmann, H., Pownall, M., Schmidt, K., Elsherif, M., Breznau, N., Robertson, O., Kalandadze, T., Yu, S., Baker, B. J., O’Mahony, A., Olsnes, J. Ø.-S., Shaw, J. J., Gjoneska, B., Yamada, Y., Röer, J. P., Murphy, J., … Evans, T. (2023). The replication crisis has led to positive structural, procedural, and community changes. Communications Psychology, 1(1). https://doi.org/10.1038/s44271-023-00003-2", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/dtvs7", + "apa": "Lakens, D. (2023). Concerns about Replicability, Theorizing, Applicability, Generalizability, and Methodology across Two Crises in Social Psychology. https://doi.org/10.31234/osf.io/dtvs7", + "auto_ref": true + }, + { + "doi": "", + "apa": "Leonelli, S. (2023). Philosophy of open science. Cambridge University Press. http://philsci-archive.pitt.edu/id/eprint/21986", + "auto_ref": false + }, + { + "doi": "10.1126/science.159.3810.56", + "apa": "Merton, R. K. (1968). The Matthew Effect in Science. Science, 159(3810), 56–63. https://doi.org/10.1126/science.159.3810.56", + "auto_ref": true + }, + { + "doi": "10.1086/354848", + "apa": "Merton, R. K. (1988). The Matthew Effect in Science, II: Cumulative Advantage and the Symbolism of Intellectual Property. Isis, 79(4), 606–623. https://doi.org/10.1086/354848", + "auto_ref": true + }, + { + "doi": "10.1038/s41562-016-0021", + "apa": "Munafò, M. R., Nosek, B. A., Bishop, D. V. M., Button, K. S., Chambers, C. D., Percie du Sert, N., Simonsohn, U., Wagenmakers, E.-J., Ware, J. J., & Ioannidis, J. P. A. (2017). A manifesto for reproducible science. Nature Human Behaviour, 1(1). https://doi.org/10.1038/s41562-016-0021", + "auto_ref": true + }, + { + "doi": "10.1146/annurev-psych-122216-011836", + "apa": "Nelson, L. D., Simmons, J., & Simonsohn, U. (2018). Psychology’s Renaissance. Annual Review of Psychology, 69(1), 511–534. https://doi.org/10.1146/annurev-psych-122216-011836", + "auto_ref": true + }, + { + "doi": "10.1146/annurev-psych-020821-114157", + "apa": "Nosek, B. A., Hardwicke, T. E., Moshontz, H., Allard, A., Corker, K. S., Dreber, A., Fidler, F., Hilgard, J., Kline Struhl, M., Nuijten, M. B., Rohrer, J. M., Romero, F., Scheel, A. M., Scherer, L. D., Schönbrodt, F. D., & Vazire, S. (2022). Replicability, Robustness, and Reproducibility in Psychological Science. Annual Review of Psychology, 73(1), 719–748. https://doi.org/10.1146/annurev-psych-020821-114157", + "auto_ref": true + }, + { + "doi": "10.1038/526182a", + "apa": "Nuzzo, R. (2015). How scientists fool themselves – and how they can stop. Nature, 526(7572), 182–185. https://doi.org/10.1038/526182a", + "auto_ref": true + }, + { + "doi": "", + "apa": "Devezer, B., & Buzbas, E. O. (2025). Minimum viable experiment to replicate. PhilSci Archive. https://philsci-archive.pitt.edu/24738/", + "auto_ref": false + }, + { + "doi": "10.1038/s41562-021-01269-4", + "apa": "Parsons, S., Azevedo, F., Elsherif, M. M., Guay, S., Shahim, O. N., Govaart, G. H., Norris, E., O’Mahony, A., Parker, A. J., Todorovic, A., Pennington, C. R., Garcia-Pelegrin, E., Lazić, A., Robertson, O., Middleton, S. L., Valentini, B., McCuaig, J., Baker, B. J., Collins, E., … Aczel, B. (2022). A community-sourced glossary of open scholarship terms. Nature Human Behaviour, 6(3), 312–318. https://doi.org/10.1038/s41562-021-01269-4", + "auto_ref": true + }, + { + "doi": "10.31222/osf.io/vhmk2", + "apa": "Penders, B. (2024). Renovating the Theatre of Persuasion. ManyLabs as Collaborative Prototypes for the Production of Credible Knowledge. https://doi.org/10.31222/osf.io/vhmk2", + "auto_ref": true + }, + { + "doi": "10.1007/s11024-023-09490-3", + "apa": "Peterson, D., & Panofsky, A. (2023). Metascience as a Scientific Social Movement. Minerva, 61(2), 147–174. https://doi.org/10.1007/s11024-023-09490-3", + "auto_ref": true + }, + { + "doi": "10.1177/10892680241235120", + "apa": "Phaf, R. H. (2024). Positive Deviance Underlies Successful Science: Normative Methodologies Risk Throwing out the Baby With the Bathwater. Review of General Psychology, 28(3), 219–236. https://doi.org/10.1177/10892680241235120", + "auto_ref": true + }, + { + "doi": "10.1177/1745691617751884", + "apa": "Vazire, S. (2018). Implications of the Credibility Revolution for Productivity, Creativity, and Progress. Perspectives on Psychological Science, 13(4), 411–417. https://doi.org/10.1177/1745691617751884", + "auto_ref": true + } + ] + }, + { + "name": "Scientific Misconduct: Fabrication and Falsification", + "description": "In order to understand and weigh in on how the Reproducibility Crisis started, we first need to understand scientific misconduct, especially data fabrication and falsification. These practices erode trust in science and distort the research record. Fabrication involves inventing data, participants, or outcomes; falsification involves altering materials, methods, measurements, images, or reporting so that findings are misrepresented. Because intent to mislead is central, these acts are distinct from questionable research practices and from honest mistakes. Recognizing the role of misconduct is therefore essential for understanding how unreliable or non-replicable studies entered the literature and contributed to the broader crisis.", + "publications": [ + { + "doi": "10.1371/journal.pone.0005738", + "apa": "Fanelli, D. (2009). How Many Scientists Fabricate and Falsify Research? A Systematic Review and Meta-Analysis of Survey Data. PLoS ONE, 4(5), e5738. https://doi.org/10.1371/journal.pone.0005738", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.1212247109", + "apa": "Fang, F. C., Steen, R. G., & Casadevall, A. (2012). Misconduct accounts for the majority of retracted scientific publications. Proceedings of the National Academy of Sciences, 109(42), 17028–17033. https://doi.org/10.1073/pnas.1212247109", + "auto_ref": true + }, + { + "doi": "10.1007/s10838-021-09555-5", + "apa": "Haven, T., & van Woudenberg, R. (2021). Explanations of Research Misconduct, and How They Hang Together. Journal for General Philosophy of Science, 52(4), 543–561. https://doi.org/10.1007/s10838-021-09555-5", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.1913039116", + "apa": "Jamieson, K. H., McNutt, M., Kiermer, V., & Sever, R. (2019). Signaling the trustworthiness of science. Proceedings of the National Academy of Sciences, 116(39), 19231–19236. https://doi.org/10.1073/pnas.1913039116", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.1918001116", + "apa": "Jamieson, K. H., McNutt, M., Kiermer, V., & Sever, R. (2019). Reply to Kornfeld and Titus: No distraction from misconduct. Proceedings of the National Academy of Sciences, 117(1), 42–42. https://doi.org/10.1073/pnas.1918001116", + "auto_ref": true + }, + { + "doi": "10.1111/dewb.12024", + "apa": "Kombe, F., Anunobi, E. N., Tshifugula, N. P., Wassenaar, D., Njadingwe, D., Mwalukore, S., Chinyama, J., Randrianasolo, B., Akindeh, P., Dlamini, P. S., Ramiandrisoa, F. N., & Ranaivo, N. (2013). Promoting Research Integrity in Africa: An African Voice of Concern on Research Misconduct and the Way Forward. Developing World Bioethics, 14(3), 158–166. Portico. https://doi.org/10.1111/dewb.12024", + "auto_ref": true + }, + { + "doi": "10.1038/537029a", + "apa": "Kornfeld, D. S., & Titus, S. L. (2016). Stop ignoring misconduct. Nature, 537(7618), 29–30. https://doi.org/10.1038/537029a", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.1917490116", + "apa": "Kornfeld, D. S., & Titus, S. L. (2019). Signaling the trustworthiness of science should not be a substitute for direct action against research misconduct. Proceedings of the National Academy of Sciences, 117(1), 41–41. https://doi.org/10.1073/pnas.1917490116", + "auto_ref": true + }, + { + "doi": "10.1177/1745691612460687", + "apa": "Stroebe, W., Postmes, T., & Spears, R. (2012). Scientific Misconduct and the Myth of Self-Correction in Science. Perspectives on Psychological Science, 7(6), 670–688. https://doi.org/10.1177/1745691612460687", + "auto_ref": true + } + ] + }, + { + "name": "Questionable research practices & their prevalence", + "description": "Questionable research practices are actions which researchers take to increase the probability of their desired result. They can be done consciously and unconsciously, distinguishing them from deliberate scientific misconduct, but still compromise research integrity since they can lead to misleading conclusions. Examples of such behaviors include p-hacking, selective reporting, and HARK-ing (Hypothesizing After the Results are Known). The ways in which researchers engage in behaviors and decision-making that increase the probability of their (consciously or unconsciously) desired result.", + "publications": [ + { + "doi": "10.1007/s10670-024-00834-3", + "apa": "Erasmus, A. (2024). p-Hacking: Its Costs and When It Is Warranted. Erkenntnis, 90(7), 2929–2950. https://doi.org/10.1007/s10670-024-00834-3", + "auto_ref": true + }, + { + "doi": "", + "apa": "Gelman, A., & Loken, E. (2013). The garden of forking paths: Why multiple comparisons can be a problem, even when there is no “fishing expedition” or “p-hacking” and the research hypothesis was posited ahead of time. Unpublished manuscript. http://www.stat.columbia.edu/~gelman/research/unpublished/p_hacking.pdf", + "auto_ref": false + }, + { + "doi": "10.31222/osf.io/aqyhg", + "apa": "Horbach, S. P. J. M., Aagaard, K., & Schneider, J. W. (2021). Meta-Research: How problematic citing practices distort science. https://doi.org/10.31222/osf.io/aqyhg", + "auto_ref": true + }, + { + "doi": "10.1016/j.respol.2017.09.004", + "apa": "Horbach, S. P. J. M. (Serge), & Halffman, W. (Willem). (2019). The extent and causes of academic text recycling or ‘self-plagiarism.’ Research Policy, 48(2), 492–502. https://doi.org/10.1016/j.respol.2017.09.004", + "auto_ref": true + }, + { + "doi": "10.1177/0956797611430953", + "apa": "John, L. K., Loewenstein, G., & Prelec, D. (2012). Measuring the Prevalence of Questionable Research Practices With Incentives for Truth Telling. Psychological Science, 23(5), 524–532. https://doi.org/10.1177/0956797611430953", + "auto_ref": true + }, + { + "doi": "10.1177/25152459241296397", + "apa": "Lengersdorff, L. L., & Lamm, C. (2025). With Low Power Comes Low Credibility? Toward a Principled Critique of Results From Underpowered Tests. Advances in Methods and Practices in Psychological Science, 8(1). https://doi.org/10.1177/25152459241296397", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/ah9wb_v3", + "apa": "Rubin, M. (2025). A brief review of research that questions the impact of questionable research practices. https://doi.org/10.31234/osf.io/ah9wb_v3", + "auto_ref": true + }, + { + "doi": "10.1093/bjps/axz050", + "apa": "Rubin, M. (2022). The Costs of HARKing. The British Journal for the Philosophy of Science, 73(2), 535–560. https://doi.org/10.1093/bjps/axz050", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/4tpk8_v2", + "apa": "Rubin, M. (2025). What is critical metascience and why is it important? https://doi.org/10.31234/osf.io/4tpk8_v2", + "auto_ref": true + }, + { + "doi": "10.1177/0956797611417632", + "apa": "Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011). False-Positive Psychology. Psychological Science, 22(11), 1359–1366. https://doi.org/10.1177/0956797611417632", + "auto_ref": true + }, + { + "doi": "10.1098/rsos.160384", + "apa": "Smaldino, P. E., & McElreath, R. (2016). The natural selection of bad science. Royal Society Open Science, 3(9), 160384. https://doi.org/10.1098/rsos.160384", + "auto_ref": true + }, + { + "doi": "10.3389/fpsyg.2016.01832", + "apa": "Wicherts, J. M., Veldkamp, C. L. S., Augusteijn, H. E. M., Bakker, M., van Aert, R. C. M., & van Assen, M. A. L. M. (2016). Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking. Frontiers in Psychology, 7. https://doi.org/10.3389/fpsyg.2016.01832", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-021-00314-9", + "apa": "Xie, Y., Wang, K., & Kong, Y. (2021). Prevalence of Research Misconduct and Questionable Research Practices: A Systematic Review and Meta-Analysis. Science and Engineering Ethics, 27(4). https://doi.org/10.1007/s11948-021-00314-9", + "auto_ref": true + } + ] + }, + { + "name": "Collection of large scale replications", + "description": "This is a collection of large scale replications that have been conducted estimating the rate of reproducibility of entire (sub)disciplines, offering a big-picture view of replication efforts and the current state of replicability across fields.", + "publications": [ + { + "doi": "10.1016/j.jebo.2023.05.009", + "apa": "Ankel-Peters, J., Fiala, N., & Neubauer, F. (2023). Do economists replicate? Journal of Economic Behavior & Organization, 212, 219–232. https://doi.org/10.1016/j.jebo.2023.05.009", + "auto_ref": true + }, + { + "doi": "10.1086/734279", + "apa": "Arel-Bundock, V., Briggs, R. C., Doucouliagos, H., Aviña, M. M., & Stanley, T. D. (2026). Quantitative Political Science Research Is Greatly Underpowered. 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F., Dreber, A., Holzmeister, F., Ho, T.-H., Huber, J., Johannesson, M., Kirchler, M., Nave, G., Nosek, B. A., Pfeiffer, T., Altmejd, A., Buttrick, N., Chan, T., Chen, Y., Forsell, E., Gampa, A., Heikensten, E., Hummer, L., Imai, T., … Wu, H. (2018). Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015. Nature Human Behaviour, 2(9), 637–644. https://doi.org/10.1038/s41562-018-0399-z", + "auto_ref": true + }, + { + "doi": "10.17016/feds.2015.083", + "apa": "Chang, A. C., & Li, P. (2015). Is Economics Research Replicable? Sixty Published Papers from Thirteen Journals Say “Usually Not.” Finance and Economics Discussion Series, 2015.0(83), 1–26. https://doi.org/10.17016/feds.2015.083", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/sa6rc", + "apa": "Clarke, B., Lee, P. Y., Schiavone, S. R., Rhemtulla, M., & Vazire, S. (2023). The Prevalence of Direct Replication Articles in Top-Ranking Psychology Journals. https://doi.org/10.31234/osf.io/sa6rc", + "auto_ref": true + }, + { + "doi": "10.1016/j.jesp.2015.10.012", + "apa": "Ebersole, C. R., Atherton, O. E., Belanger, A. L., Skulborstad, H. M., Allen, J. M., Banks, J. B., Baranski, E., Bernstein, M. J., Bonfiglio, D. B. V., Boucher, L., Brown, E. R., Budiman, N. I., Cairo, A. H., Capaldi, C. A., Chartier, C. R., Chung, J. M., Cicero, D. C., Coleman, J. A., Conway, J. G., … Nosek, B. A. (2016). Many Labs 3: Evaluating participant pool quality across the academic semester via replication. Journal of Experimental Social Psychology, 67, 68–82. https://doi.org/10.1016/j.jesp.2015.10.012", + "auto_ref": true + }, + { + "doi": "10.1177/2515245920958687", + "apa": "Ebersole, C. R., Mathur, M. B., Baranski, E., Bart-Plange, D.-J., Buttrick, N. R., Chartier, C. R., Corker, K. S., Corley, M., Hartshorne, J. K., IJzerman, H., Lazarević, L. B., Rabagliati, H., Ropovik, I., Aczel, B., Aeschbach, L. F., Andrighetto, L., Arnal, J. D., Arrow, H., Babincak, P., … Nosek, B. A. (2020). Many Labs 5: Testing Pre-Data-Collection Peer Review as an Intervention to Increase Replicability. Advances in Methods and Practices in Psychological Science, 3(3), 309–331. https://doi.org/10.1177/2515245920958687", + "auto_ref": true + }, + { + "doi": "10.7554/eLife.71601", + "apa": "Errington, T. M., Mathur, M., Soderberg, C. K., Denis, A., Perfito, N., Iorns, E., & Nosek, B. A. (2021). Investigating the replicability of preclinical cancer biology. ELife, 10. CLOCKSS. https://doi.org/10.7554/elife.71601", + "auto_ref": true + }, + { + "doi": "10.1002/aepp.13386", + "apa": "Finger, R., Grebitus, C., & Henningsen, A. (2023). Replications in agricultural economics. Applied Economic Perspectives and Policy, 45(3), 1258–1274. Portico. https://doi.org/10.1002/aepp.13386", + "auto_ref": true + }, + { + "doi": "10.17605/OSF.IO/WFC6U", + "apa": "Christopherson, C. D., Hildebrandt, L., Adeyemi Adetula, Wiggins, B. J., McLaughlin, H., Hurst, M. A., IJzerman, H., Levitan, C., Legate, N., Pazda, A., Kaylis Hase, VanBenschoten, A., Fallon, M., LePine, S., Gervais, H., Lazarevic, L., Chartier, C. R., Corker, K. S., France, H., … Wagge, J. (2013). Collaborative Replications and Education Project (CREP). OSF. https://doi.org/10.17605/OSF.IO/WFC6U", + "auto_ref": true + }, + { + "doi": "10.1177/1745691620979806", + "apa": "Hardwicke, T. E., Thibault, R. T., Kosie, J. E., Wallach, J. D., Kidwell, M. C., & Ioannidis, J. P. A. (2021). Estimating the Prevalence of Transparency and Reproducibility-Related Research Practices in Psychology (2014–2017). Perspectives on Psychological Science, 17(1), 239–251. https://doi.org/10.1177/1745691620979806", + "auto_ref": true + }, + { + "doi": "10.1086/506236", + "apa": "Kelly, C. D. (2006). Replicating Empirical Research In Behavioral Ecology: How And Why It Should Be Done But Rarely Ever Is. The Quarterly Review of Biology, 81(3), 221–236. https://doi.org/10.1086/506236", + "auto_ref": true + }, + { + "doi": "10.7717/peerj.7654", + "apa": "Kelly, C. D. (2019). Rate and success of study replication in ecology and evolution. PeerJ, 7, e7654. Portico. https://doi.org/10.7717/peerj.7654", + "auto_ref": true + }, + { + "doi": "10.1027/1864-9335/a000178", + "apa": "Klein, R. A., Ratliff, K. A., Vianello, M., Adams, R. B., Bahník, Š., Bernstein, M. J., Bocian, K., Brandt, M. J., Brooks, B., Brumbaugh, C. C., Cemalcilar, Z., Chandler, J., Cheong, W., Davis, W. E., Devos, T., Eisner, M., Frankowska, N., Furrow, D., Galliani, E. M., … Nosek, B. A. (2014). Investigating Variation in Replicability. Social Psychology, 45(3), 142–152. https://doi.org/10.1027/1864-9335/a000178", + "auto_ref": true + }, + { + "doi": "10.1177/2515245918810225", + "apa": "Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., Aveyard, M., Axt, J. R., Babalola, M. T., Bahník, Š., Batra, R., Berkics, M., Bernstein, M. J., Berry, D. R., Bialobrzeska, O., Binan, E. D., Bocian, K., Brandt, M. J., Busching, R., … Nosek, B. A. (2018). Many Labs 2: Investigating Variation in Replicability Across Samples and Settings. Advances in Methods and Practices in Psychological Science, 1(4), 443–490. https://doi.org/10.1177/2515245918810225", + "auto_ref": true + }, + { + "doi": "10.5070/g6011135", + "apa": "Kobrock, K., & Roettger, T. B. (2023). Assessing the replication landscape in experimental linguistics. Glossa Psycholinguistics, 2(1). https://doi.org/10.5070/g6011135", + "auto_ref": true + }, + { + "doi": "10.3102/0013189X14545513", + "apa": "Makel, M. C., & Plucker, J. A. (2014). Facts Are More Important Than Novelty. 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Replication in Second Language Research: Narrative and Systematic Reviews and Recommendations for the Field. Language Learning, 68(2), 321–391. Portico. https://doi.org/10.1111/lang.12286", + "auto_ref": true + }, + { + "doi": "10.1177/1477370815578197", + "apa": "McNeeley, S., & Warner, J. J. (2015). Replication in criminology: A necessary practice. European Journal of Criminology, 12(5), 581–597. https://doi.org/10.1177/1477370815578197", + "auto_ref": true + }, + { + "doi": "10.1016/j.respol.2018.07.019", + "apa": "Mueller-Langer, F., Fecher, B., Harhoff, D., & Wagner, G. G. (2019). Replication studies in economics—How many and which papers are chosen for replication, and why? Research Policy, 48(1), 62–83. https://doi.org/10.1016/j.respol.2018.07.019", + "auto_ref": true + }, + { + "doi": "10.1177/1745691612462588", + "apa": "(2012). An Open, Large-Scale, Collaborative Effort to Estimate the Reproducibility of Psychological Science. 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European Journal for Philosophy of Science, 15(1). https://doi.org/10.1007/s13194-024-00629-x", + "auto_ref": true + }, + { + "doi": "10.1037/teo0000301", + "apa": "Sanbonmatsu, D. M., Neufeld, B., & Posavac, S. S. (2025). There is no theory crisis in psychological science. Journal of Theoretical and Philosophical Psychology. https://doi.org/10.1037/teo0000301", + "auto_ref": true + }, + { + "doi": "10.1016/j.tourman.2024.105061", + "apa": "Souza-Neto, V., & Moyle, B. (2025). Preregistration is not a panacea, but why? A rejoinder to “infusing preregistration into tourism research.” Tourism Management, 107, 105061. https://doi.org/10.1016/j.tourman.2024.105061", + "auto_ref": true + }, + { + "doi": "10.5281/zenodo.17136864", + "apa": "Ulpts, S., Bartscherer, S. F., Penders, B., & Nelson, N. (2025). Epistemic oligarchies: capture and concentration through science reform. Zenodo. https://doi.org/10.5281/ZENODO.17136864", + "auto_ref": true + } + ] + } + ] + }, + { + "number": 2, + "name": "Conceptual and Statistical Knowledge", + "description": "Attainment of a grounding in fundamental statistics, measurement, and its implications encompassing conceptual knowledge, application, interpretation and communication of statistical analyses. There are 8 sub-clusters which aim to further parse the learning and teaching process:", + "sub_clusters": [ + { + "name": "Effect sizes, statistical power, simulations, & confidence intervals.", + "description": "Statistics are more than p-values and we need to use other benchmarks to determine the statistical and practical relevance of an effect. 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Quantitative Political Science Research Is Greatly Underpowered. The Journal of Politics, 88(1), 36–46. https://doi.org/10.1086/734279", + "auto_ref": true + }, + { + "doi": "10.1038/s41562-021-01143-3", + "apa": "Bryan, C. J., Tipton, E., & Yeager, D. S. (2021). Behavioural science is unlikely to change the world without a heterogeneity revolution. Nature Human Behaviour, 5(8), 980–989. https://doi.org/10.1038/s41562-021-01143-3", + "auto_ref": true + }, + { + "doi": "10.5334/joc.10", + "apa": "Brysbaert, M., & Stevens, M. (2018). Power Analysis and Effect Size in Mixed Effects Models: A Tutorial. Journal of Cognition, 1(1). https://doi.org/10.5334/joc.10", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/e3afx", + "apa": "Buchanan, E. M., Elsherif, M. M., Geller, J., Aberson, C., Gurkan, N., Ambrosini, E., Heyman, T., Montefinese, M., vanpaemel, wolf, Barzykowski, K., Batres, C., Fellnhofer, K., Huang, G., McFall, J. P., Ribeiro, G., Röer, J. P., Ulloa Fulgeri, J. L., Roettger, T. B., Valentine, K. D., … Lewis, S. C. (2023). Accuracy in Parameter Estimation and Simulation Approaches for Sample Size Planning with Multiple Stimuli. https://doi.org/10.31219/osf.io/e3afx", + "auto_ref": true + }, + { + "doi": "10.1038/nrn3475", + "apa": "Button, K. S., Ioannidis, J. P. A., Mokrysz, C., Nosek, B. A., Flint, J., Robinson, E. S. J., & Munafò, M. R. (2013). Power failure: why small sample size undermines the reliability of neuroscience. Nature Reviews Neuroscience, 14(5), 365–376. https://doi.org/10.1038/nrn3475", + "auto_ref": true + }, + { + "doi": "", + "apa": "Caldwell, A. R., Lakens, D., Parlett‑Pelleriti, C. M., Prochilo, G., & Aust, F. (2022). Power analysis with Superpower. https://aaroncaldwell.us/SuperpowerBook/", + "auto_ref": false + }, + { + "doi": "10.1177/2515245920965119", + "apa": "DeBruine, L. M., & Barr, D. J. (2021). Understanding Mixed-Effects Models Through Data Simulation. Advances in Methods and Practices in Psychological Science, 4(1). https://doi.org/10.1177/2515245920965119", + "auto_ref": true + }, + { + "doi": "10.1007/s10654-016-0149-3", + "apa": "Greenland, S., Senn, S. J., Rothman, K. J., Carlin, J. B., Poole, C., Goodman, S. N., & Altman, D. G. (2016). Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations. European Journal of Epidemiology, 31(4), 337–350. https://doi.org/10.1007/s10654-016-0149-3", + "auto_ref": true + }, + { + "doi": "10.20982/tqmp.09.2.p043", + "apa": "Hallgren, K. A. (2013). Conducting Simulation Studies in the R Programming Environment. Tutorials in Quantitative Methods for Psychology, 9(2), 43–60. https://doi.org/10.20982/tqmp.09.2.p043", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.2403490121", + "apa": "Holzmeister, F., Johannesson, M., Böhm, R., Dreber, A., Huber, J., & Kirchler, M. (2024). Heterogeneity in effect size estimates. Proceedings of the National Academy of Sciences, 121(32). https://doi.org/10.1073/pnas.2403490121", + "auto_ref": true + }, + { + "doi": "10.3389/fpsyg.2013.00863", + "apa": "Lakens, D. (2013). Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs. Frontiers in Psychology, 4. https://doi.org/10.3389/fpsyg.2013.00863", + "auto_ref": true + }, + { + "doi": "10.1525/collabra.33267", + "apa": "Lakens, D. (2022). Sample Size Justification. Collabra: Psychology, 8(1). https://doi.org/10.1525/collabra.33267", + "auto_ref": true + }, + { + "doi": "10.1177/25152459241296397", + "apa": "Lengersdorff, L. L., & Lamm, C. (2025). With Low Power Comes Low Credibility? Toward a Principled Critique of Results From Underpowered Tests. Advances in Methods and Practices in Psychological Science, 8(1). https://doi.org/10.1177/25152459241296397", + "auto_ref": true + }, + { + "doi": "10.1037/met0000126", + "apa": "Pek, J., & Flora, D. B. (2018). Reporting effect sizes in original psychological research: A discussion and tutorial. Psychological Methods, 23(2), 208–225. https://doi.org/10.1037/met0000126", + "auto_ref": true + }, + { + "doi": "10.1177/1745691614528519", + "apa": "Perugini, M., Gallucci, M., & Costantini, G. (2014). Safeguard Power as a Protection Against Imprecise Power Estimates. Perspectives on Psychological Science, 9(3), 319–332. https://doi.org/10.1177/1745691614528519", + "auto_ref": true + }, + { + "doi": "10.1177/01461672211030811", + "apa": "Wegener, D. T., Fabrigar, L. R., Pek, J., & Hoisington-Shaw, K. (2021). Evaluating Research in Personality and Social Psychology: Considerations of Statistical Power and Concerns About False Findings. Personality and Social Psychology Bulletin, 48(7), 1105–1117. https://doi.org/10.1177/01461672211030811", + "auto_ref": true + }, + { + "doi": "10.32872/spb.9981", + "apa": "Wilson, B. M., & Wixted, J. T. (2023). On the importance of modeling the invisible world of underlying effect sizes. Social Psychological Bulletin, 18. https://doi.org/10.32872/spb.9981", + "auto_ref": true + } + ] + }, + { + "name": "Exploratory and confirmatory analyses", + "description": "Confirmatory analyses test a priori hypotheses against a pre-specified analysis plan (ideally preregistered/Registered Report); any deviations are documented. Exploratory analyses probe patterns, generate hypotheses, and build models after seeing the data.", + "publications": [ + { + "doi": "10.1515/9781400884940", + "apa": "Chambers, C. (2017). The Seven Deadly Sins of Psychology. https://doi.org/10.1515/9781400884940", + "auto_ref": true + }, + { + "doi": "", + "apa": "Feest, U., & Devezer, B. (2025). Toward a more accurate notion of exploratory research (and why it matters). PhilSci Archive. https://philsci-archive.pitt.edu/24482/", + "auto_ref": false + }, + { + "doi": "10.3389/fpsyg.2022.1020770", + "apa": "Jacobucci, R. (2022). A critique of using the labels confirmatory and exploratory in modern psychological research. Frontiers in Psychology, 13. https://doi.org/10.3389/fpsyg.2022.1020770", + "auto_ref": true + }, + { + "doi": "10.1017/S1049096516000810", + "apa": "Lin, W., & Green, D. P. (2016). Standard Operating Procedures: A Safety Net for Pre-Analysis Plans. Political Science and Politics, 49(3), 495–500. https://doi.org/10.1017/s1049096516000810", + "auto_ref": true + }, + { + "doi": "10.1080/09515089.2022.2113771", + "apa": "Rubin, M., & Donkin, C. (2022). Exploratory hypothesis tests can be more compelling than confirmatory hypothesis tests. Philosophical Psychology, 37(8), 2019–2047. https://doi.org/10.1080/09515089.2022.2113771", + "auto_ref": true + }, + { + "doi": "10.1177/1745691620966796", + "apa": "Szollosi, A., & Donkin, C. (2021). Arrested Theory Development: The Misguided Distinction Between Exploratory and Confirmatory Research. Perspectives on Psychological Science, 16(4), 717–724. https://doi.org/10.1177/1745691620966796", + "auto_ref": true + }, + { + "doi": "10.1177/1745691618771357", + "apa": "Wagenmakers, E.-J., Dutilh, G., & Sarafoglou, A. (2018). The Creativity-Verification Cycle in Psychological Science: New Methods to Combat Old Idols. Perspectives on Psychological Science, 13(4), 418–427. https://doi.org/10.1177/1745691618771357", + "auto_ref": true + }, + { + "doi": "10.1177/1745691612463078", + "apa": "Wagenmakers, E.-J., Wetzels, R., Borsboom, D., van der Maas, H. L. J., & Kievit, R. A. (2012). An Agenda for Purely Confirmatory Research. Perspectives on Psychological Science, 7(6), 632–638. https://doi.org/10.1177/1745691612463078", + "auto_ref": true + } + ] + }, + { + "name": "Limitations and benefits of NHST, Bayesian & Likelihood approaches.", + "description": "Next to frequentist statistics, there are other quantitative approaches, each with different assumptions and goals. This subcluster summarizes benefits and limitations of each one.", + "publications": [ + { + "doi": "10.1177/0956797613504966", + "apa": "Cumming, G. (2013). The New Statistics. Psychological Science, 25(1), 7–29. https://doi.org/10.1177/0956797613504966", + "auto_ref": true + }, + { + "doi": "10.3758/s13423-017-1317-5", + "apa": "Etz, A., Gronau, Q. F., Dablander, F., Edelsbrunner, P. A., & Baribault, B. (2017). How to become a Bayesian in eight easy steps: An annotated reading list. Psychonomic Bulletin & Review, 25(1), 219–234. https://doi.org/10.3758/s13423-017-1317-5", + "auto_ref": true + }, + { + "doi": "10.1007/s10654-016-0149-3", + "apa": "Greenland, S., Senn, S. J., Rothman, K. J., Carlin, J. B., Poole, C., Goodman, S. N., & Altman, D. G. (2016). Statistical tests, P values, confidence intervals, and power: a guide to misinterpretations. European Journal of Epidemiology, 31(4), 337–350. https://doi.org/10.1007/s10654-016-0149-3", + "auto_ref": true + }, + { + "doi": "10.2307/2291091", + "apa": "Kass, R. E., & Raftery, A. E. (1995). Bayes Factors. Journal of the American Statistical Association, 90(430), 773–795. https://doi.org/10.1080/01621459.1995.10476572", + "auto_ref": true + }, + { + "doi": "10.1038/s41593-020-0660-4", + "apa": "Keysers, C., Gazzola, V., & Wagenmakers, E.-J. (2020). Using Bayes factor hypothesis testing in neuroscience to establish evidence of absence. Nature Neuroscience, 23(7), 788–799. https://doi.org/10.1038/s41593-020-0660-4", + "auto_ref": true + }, + { + "doi": "10.1038/506150a", + "apa": "Nuzzo, R. (2014). Scientific method: Statistical errors. Nature, 506(7487), 150–152. https://doi.org/10.1038/506150a", + "auto_ref": true + }, + { + "doi": "10.1177/1745691618771357", + "apa": "Wagenmakers, E.-J., Dutilh, G., & Sarafoglou, A. (2018). The Creativity-Verification Cycle in Psychological Science: New Methods to Combat Old Idols. Perspectives on Psychological Science, 13(4), 418–427. https://doi.org/10.1177/1745691618771357", + "auto_ref": true + }, + { + "doi": "10.1257/aeri.20190252", + "apa": "Abadie, A. (2020). Statistical Nonsignificance in Empirical Economics. American Economic Review: Insights, 2(2), 193–208. https://doi.org/10.1257/aeri.20190252", + "auto_ref": true + }, + { + "doi": "10.1007/s11186-025-09614-6", + "apa": "Gelman, A., & Higgs, M. (2025). Interrogating the “cargo cult science” metaphor. Theory and Society, 54(2), 197–207. https://doi.org/10.1007/s11186-025-09614-6", + "auto_ref": true + }, + { + "doi": "10.1037/mot0000398", + "apa": "Harmon-Jones, E., Harmon-Jones, C., Amodio, D. M., Gable, P. A., & Schmeichel, B. J. (2025). Valid replications require valid methods: Recommendations for best methodological practices with lab experiments. Motivation Science, 11(3), 235–245. https://doi.org/10.1037/mot0000398", + "auto_ref": true + }, + { + "doi": "10.1177/25152459241296397", + "apa": "Lengersdorff, L. L., & Lamm, C. (2025). With Low Power Comes Low Credibility? Toward a Principled Critique of Results From Underpowered Tests. Advances in Methods and Practices in Psychological Science, 8(1). https://doi.org/10.1177/25152459241296397", + "auto_ref": true + } + ] + }, + { + "name": "Philosophy of science", + "description": "Approaches to assess the reliability of scientific theories, reasoning, and methods attempting to understand its ability to make predictions about the natural and social world. Introduces how differing philosophies (positivist, post-positivist, constructivist, etc.) influence what scientists consider valid evidence and how open science challenges some traditional norms.", + "publications": [ + { + "doi": "10.1177/03616843211036460", + "apa": "Bennett, E. A. (2021). Open Science From a Qualitative, Feminist Perspective: Epistemological Dogmas and a Call for Critical Examination. Psychology of Women Quarterly, 45(4), 448–456. https://doi.org/10.1177/03616843211036460", + "auto_ref": true + }, + { + "doi": "10.1177/16094069211034641", + "apa": "Class, B., de Bruyne, M., Wuillemin, C., Donzé, D., & Claivaz, J.-B. (2021). Towards Open Science for the Qualitative Researcher: From a Positivist to an Open Interpretation. International Journal of Qualitative Methods, 20. https://doi.org/10.1177/16094069211034641", + "auto_ref": true + }, + { + "doi": "", + "apa": "Feest, U., & Devezer, B. (2025). Toward a more accurate notion of exploratory research (and why it matters). PhilSci Archive. https://philsci-archive.pitt.edu/24482/", + "auto_ref": false + }, + { + "doi": "10.31219/osf.io/ga5fb_v1", + "apa": "Field, S. M., & Pownall, M. (2025). Subjectivity is a Feature, not a Flaw: A Call to Unsilence the Human Element in Science. https://doi.org/10.31219/osf.io/ga5fb_v1", + "auto_ref": true + }, + { + "doi": "10.1177/1745691620970585", + "apa": "Guest, O., & Martin, A. E. (2021). How Computational Modeling Can Force Theory Building in Psychological Science. Perspectives on Psychological Science, 16(4), 789–802. https://doi.org/10.1177/1745691620970585", + "auto_ref": true + }, + { + "doi": "10.1007/s42113-023-00193-2", + "apa": "Guest, O. (2024). What Makes a Good Theory, and How Do We Make a Theory Good? Computational Brain & Behavior, 7(4), 508–522. https://doi.org/10.1007/s42113-023-00193-2", + "auto_ref": true + }, + { + "doi": "10.1037/amp0001300", + "apa": "Hutmacher, F., & Franz, D. J. (2025). Approaching psychology’s current crises by exploring the vagueness of psychological concepts: Recommendations for advancing the discipline. American Psychologist, 80(2), 220–231. https://doi.org/10.1037/amp0001300", + "auto_ref": true + }, + { + "doi": "10.1037/cap0000223", + "apa": "Jamieson, R. K., & Pexman, P. M. (2020). Moving beyond 20 questions: We (still) need stronger psychological theory. Canadian Psychology / Psychologie Canadienne, 61(4), 273–280. https://doi.org/10.1037/cap0000223", + "auto_ref": true + }, + { + "doi": "10.1017/psa.2022.45", + "apa": "Leonelli, S. (2022). Open Science and Epistemic Diversity: Friends or Foes? Philosophy of Science, 89(5), 991–1001. https://doi.org/10.1017/psa.2022.45", + "auto_ref": true + }, + { + "doi": "", + "apa": "Leonelli, S. (2023). Philosophy of open science. Cambridge University Press. http://philsci-archive.pitt.edu/id/eprint/21986", + "auto_ref": false + }, + { + "doi": "", + "apa": "Mackenzie, N., & Knipe, S. (2006). Research dilemmas: Paradigms, methods and methodology. Issues in Educational Research, 16(2), 193–205. http://www.iier.org.au/iier16/mackenzie.html", + "auto_ref": false + }, + { + "doi": "10.1177/10892680221083876", + "apa": "Malich, L., & Rehmann-Sutter, C. (2022). Metascience Is Not Enough – A Plea for Psychological Humanities in the Wake of the Replication Crisis. Review of General Psychology, 26(2), 261–273. https://doi.org/10.1177/10892680221083876", + "auto_ref": true + }, + { + "doi": "10.3389/fpsyg.2024.1390233", + "apa": "Mayrhofer, R., Büchner, I. C., & Hevesi, J. (2024). The quantitative paradigm and the nature of the human mind. The replication crisis as an epistemological crisis of quantitative psychology in view of the ontic nature of the psyche. Frontiers in Psychology, 15. https://doi.org/10.3389/fpsyg.2024.1390233", + "auto_ref": true + }, + { + "doi": "10.1086/288135", + "apa": "Meehl, P. E. (1967). Theory-Testing in Psychology and Physics: A Methodological Paradox. Philosophy of Science, 34(2), 103–115. https://doi.org/10.1086/288135", + "auto_ref": true + }, + { + "doi": "10.1080/13803611.2024.2314526", + "apa": "Pownall, M. (2024). Is replication\n possible\n in qualitative research? A response to Makel et al. (2022). Educational Research and Evaluation, 29(1–2), 104–110. https://doi.org/10.1080/13803611.2024.2314526", + "auto_ref": true + }, + { + "doi": "10.1016/j.cub.2021.11.027", + "apa": "Press, C., Yon, D., & Heyes, C. (2022). Building better theories. Current Biology, 32(1), R13–R17. https://doi.org/10.1016/j.cub.2021.11.027", + "auto_ref": true + }, + { + "doi": "10.36850/mr7", + "apa": "Steltenpohl, C. N., Lustick, H., Meyer, M. S., Lee, L. E., Stegenga, S. M., Standiford Reyes, L., & Renbarger, R. L. (2023). Rethinking Transparency and Rigor from a Qualitative Open Science Perspective. Journal of Trial and Error, 4(1), 47–59. KB. https://doi.org/10.36850/mr7", + "auto_ref": true + }, + { + "doi": "10.1038/s44159-022-00031-5", + "apa": "van Rooij, I. (2022). Psychological models and their distractors. Nature Reviews Psychology, 1(3), 127–128. https://doi.org/10.1038/s44159-022-00031-5", + "auto_ref": true + }, + { + "doi": "10.1017/S0140525X20001685", + "apa": "Yarkoni, T. (2020). The generalizability crisis. Behavioral and Brain Sciences, 45. https://doi.org/10.1017/s0140525x20001685", + "auto_ref": true + }, + { + "doi": "10.1017/CBO9780511621123", + "apa": "Lakatos, I. (1978). The Methodology of Scientific Research Programmes. https://doi.org/10.1017/cbo9780511621123", + "auto_ref": true + } + ] + }, + { + "name": "Questionable measurement practices (QMPs), validity & reliability issues.", + "description": "The quality of our measures impacts the validity of our results, and offers another avenue for us to address potential questionable practices. Examines how measurement choices shape the credibility of findings. Addresses Questionable Measurement Practices (QMPs) like ad-hoc scale trimming, unvalidated instruments, poor reliability reporting, ignored measurement invariance, and their impact on construct validity, reliability, and generalizability.", + "publications": [ + { + "doi": "10.1177/2515245920952393", + "apa": "Flake, J. K., & Fried, E. I. (2020). Measurement Schmeasurement: Questionable Measurement Practices and How to Avoid Them. Advances in Methods and Practices in Psychological Science, 3(4), 456–465. https://doi.org/10.1177/2515245920952393", + "auto_ref": true + }, + { + "doi": "10.1177/1948550617693063", + "apa": "Flake, J. K., Pek, J., & Hehman, E. (2017). Construct Validation in Social and Personality Research. Social Psychological and Personality Science, 8(4), 370–378. https://doi.org/10.1177/1948550617693063", + "auto_ref": true + }, + { + "doi": "10.1037/amp0001300", + "apa": "Hutmacher, F., & Franz, D. J. (2025). Approaching psychology’s current crises by exploring the vagueness of psychological concepts: Recommendations for advancing the discipline. American Psychologist, 80(2), 220–231. https://doi.org/10.1037/amp0001300", + "auto_ref": true + }, + { + "doi": "10.1177/2515245919882903", + "apa": "Hussey, I., & Hughes, S. (2020). Hidden Invalidity Among 15 Commonly Used Measures in Social and Personality Psychology. Advances in Methods and Practices in Psychological Science, 3(2), 166–184. https://doi.org/10.1177/2515245919882903", + "auto_ref": true + }, + { + "doi": "10.15626/MP.2020.2577", + "apa": "Parsons, S. (2022). Exploring reliability heterogeneity with multiverse analyses: Data processing decisions unpredictably influence measurement reliability. Meta-Psychology, 6. https://doi.org/10.15626/mp.2020.2577", + "auto_ref": true + }, + { + "doi": "10.1177/2515245919879695", + "apa": "Parsons, S., Kruijt, A.-W., & Fox, E. (2019). Psychological Science Needs a Standard Practice of Reporting the Reliability of Cognitive-Behavioral Measurements. Advances in Methods and Practices in Psychological Science, 2(4), 378–395. https://doi.org/10.1177/2515245919879695", + "auto_ref": true + }, + { + "doi": "10.1037/abn0000184", + "apa": "Rodebaugh, T. L., Scullin, R. B., Langer, J. K., Dixon, D. J., Huppert, J. D., Bernstein, A., Zvielli, A., & Lenze, E. J. (2016). Unreliability as a threat to understanding psychopathology: The cautionary tale of attentional bias. Journal of Abnormal Psychology, 125(6), 840–851. https://doi.org/10.1037/abn0000184", + "auto_ref": true + }, + { + "doi": "10.1037/met0000770", + "apa": "Heyman, T., Pronizius, E., Lewis, S. C., Acar, O. A., Adamkovič, M., Ambrosini, E., Antfolk, J., Barzykowski, K., Baskin, E., Batres, C., Boucher, L., Boudesseul, J., Brandstätter, E., Collins, W. M., Filipović Ðurđević, D., Egan, C., Era, V., Ferreira, P., Fini, C., … Buchanan, E. M. (2025). Crowdsourcing multiverse analyses to explore the impact of different data-processing and analysis decisions: A tutorial. Psychological Methods. https://doi.org/10.1037/met0000770", + "auto_ref": true + } + ] + }, + { + "name": "Research design, sampling methods, & its implications for inferences.", + "description": "How design choices and sampling strategies shape bias, precision, and generalizability. Includes threats to validity (internal/external), power and sample-size planning, selection bias, clustering/design effects, weighting, and transparent reporting/preregistration. Design and sampling decisions determine the credibility and scope of statistical inference. This sub-cluster emphasizes adequate power and sample-size planning (e.g., safeguard power), transparent pre-analysis planning to constrain researcher degrees of freedom, and rigorous, valid methods as prerequisites for meaningful replication—reducing bias, increasing precision, and improving generalizability across lab and field work.", + "publications": [ + { + "doi": "10.1177/1948550615584199", + "apa": "Gervais, W. M., Jewell, J. A., Najle, M. B., & Ng, B. K. L. (2015). A Powerful Nudge? Presenting Calculable Consequences of Underpowered Research Shifts Incentives Toward Adequately Powered Designs. Social Psychological and Personality Science, 6(7), 847–854. https://doi.org/10.1177/1948550615584199", + "auto_ref": true + }, + { + "doi": "10.1037/mot0000398", + "apa": "Harmon-Jones, E., Harmon-Jones, C., Amodio, D. M., Gable, P. A., & Schmeichel, B. J. (2025). Valid replications require valid methods: Recommendations for best methodological practices with lab experiments. Motivation Science, 11(3), 235–245. https://doi.org/10.1037/mot0000398", + "auto_ref": true + }, + { + "doi": "10.1177/1745691614528519", + "apa": "Perugini, M., Gallucci, M., & Costantini, G. (2014). Safeguard Power as a Protection Against Imprecise Power Estimates. Perspectives on Psychological Science, 9(3), 319–332. https://doi.org/10.1177/1745691614528519", + "auto_ref": true + }, + { + "doi": "10.3389/fpsyg.2016.01832", + "apa": "Wicherts, J. M., Veldkamp, C. L. S., Augusteijn, H. E. M., Bakker, M., van Aert, R. C. M., & van Assen, M. A. L. M. (2016). Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking. Frontiers in Psychology, 7. https://doi.org/10.3389/fpsyg.2016.01832", + "auto_ref": true + } + ] + }, + { + "name": "The logic of null hypothesis testing, p-values, Type I and II errors (and when and why they might happen).", + "description": "Frequentist statistics are typically the default in quantitative research. They come with certain assumptions and implications, as well as often being misinterpreted. Frequentist statistics are typically the default in much quantitative research, but they are often misinterpreted. This sub-cluster clarifies the logic of NHST, the meaning of p-values, and when and why Type I and Type II errors arise, extending to Type S and Type M errors. It links these to design and power choices and outlines practical steps for better inference and reporting.", + "publications": [ + { + "doi": "10.4103%2F0972-6748.62274", + "apa": "Banerjee, A., Chitnis, U., Jadhav, S., Bhawalkar, J., & Chaudhury, S. (2009). Hypothesis testing, type I and type II errors. Industrial Psychiatry Journal, 18(2), 127. https://doi.org/10.4103/0972-6748.62274", + "auto_ref": true + }, + { + "doi": "10.1093/bjps/axy051", + "apa": "Bird, A. (2021). Understanding the Replication Crisis as a Base Rate Fallacy. The British Journal for the Philosophy of Science, 72(4), 965–993. https://doi.org/10.1093/bjps/axy051", + "auto_ref": true + }, + { + "doi": "10.1037/0003-066X.49.12.997", + "apa": "Cohen, J. (1994). The earth is round (p < .05). American Psychologist, 49(12), 997–1003. https://doi.org/10.1037/0003-066x.49.12.997", + "auto_ref": true + }, + { + "doi": "10.36850/4d35-44bd", + "apa": "Rubin, M. (2024). Type I Error Rates are Not Usually Inflated. Journal of Trial and Error, 4(2). KB. https://doi.org/10.36850/4d35-44bd", + "auto_ref": true + }, + { + "doi": "10.1177/1745691614551642", + "apa": "Gelman, A., & Carlin, J. (2014). Beyond Power Calculations. Perspectives on Psychological Science, 9(6), 641–651. https://doi.org/10.1177/1745691614551642", + "auto_ref": true + }, + { + "doi": "10.1007/s11186-025-09614-6", + "apa": "Gelman, A., & Higgs, M. (2025). Interrogating the “cargo cult science” metaphor. Theory and Society, 54(2), 197–207. https://doi.org/10.1007/s11186-025-09614-6", + "auto_ref": true + }, + { + "doi": "10.4135/9781412986311.n21", + "apa": "Gigerenzer, G., Krauss, S., & Vitouch, O. (2004). The Null Ritual: What You Always Wanted to Know About Significance Testing but\n Were Afraid to Ask. The SAGE Handbook of Quantitative Methodology for the Social Sciences, 392–409. https://doi.org/10.4135/9781412986311.n21", + "auto_ref": true + }, + { + "doi": "10.1016/j.socec.2004.09.033", + "apa": "Gigerenzer, G. (2004). Mindless statistics. The Journal of Socio-Economics, 33(5), 587–606. https://doi.org/10.1016/j.socec.2004.09.033", + "auto_ref": true + }, + { + "doi": "", + "apa": "Lakens, D. Improving your statistical inferences. Online course. https://www.coursera.org/learn/statistical-inferences", + "auto_ref": false + }, + { + "doi": "10.1177/25152459241296397", + "apa": "Lengersdorff, L. L., & Lamm, C. (2025). With Low Power Comes Low Credibility? Toward a Principled Critique of Results From Underpowered Tests. Advances in Methods and Practices in Psychological Science, 8(1). https://doi.org/10.1177/25152459241296397", + "auto_ref": true + }, + { + "doi": "10.1016/j.metip.2024.100140", + "apa": "Rubin, M. (2024). Inconsistent multiple testing corrections: The fallacy of using family-based error rates to make inferences about individual hypotheses. Methods in Psychology, 10, 100140. https://doi.org/10.1016/j.metip.2024.100140", + "auto_ref": true + }, + { + "doi": "10.1080/00031305.2016.1154108", + "apa": "Wasserstein, R. L., & Lazar, N. A. (2016). The ASA Statement on\n p\n -Values: Context, Process, and Purpose. The American Statistician, 70(2), 129–133. https://doi.org/10.1080/00031305.2016.1154108", + "auto_ref": true + } + ] + } + ] + }, + { + "number": 3, + "name": "Ways of Working", + "description": "Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:", + "sub_clusters": [ + { + "name": "Qualitative research", + "description": "This section includes key introductory and methodological texts on designing and conducting qualitative research. These sources provide guidance on research planning, data collection, analysis techniques, and theoretical foundations relevant for beginners and experienced researchers alike.", + "publications": [ + { + "doi": "10.4135/9781526485045", + "apa": "Barbour, R. (2014). Introducing Qualitative Research: A Student’s Guide. https://doi.org/10.4135/9781526485045", + "auto_ref": true + }, + { + "doi": "", + "apa": "Braun, V., & Clarke, V. (2013). Successful qualitative research: A practical guide for beginners. SAGE Publications. ISBN: 9781847875815", + "auto_ref": false + }, + { + "doi": "", + "apa": "Denzin, N. K., & Lincoln, Y. S. (Eds.). (2023). The SAGE handbook of qualitative research (6th ed.). SAGE Publications.", + "auto_ref": false + }, + { + "doi": "10.4135/9781529622737", + "apa": "Flick, U. (2018). Designing Qualitative Research. https://doi.org/10.4135/9781529622737", + "auto_ref": true + }, + { + "doi": "", + "apa": "Kumar, R. (2019). Research methodology: A step-by-step guide for beginners (5th ed.). SAGE Publications.", + "auto_ref": false + } + ] + }, + { + "name": "Adversarial collaborations", + "description": "Adversarial collaborations typically include two (or more) groups of researchers addressing the same research question with conflicting hypotheses - e.g., one group expects an effect to exist, while another does not.", + "publications": [ + { + "doi": "10.1016/j.jpubeco.2004.06.013", + "apa": "Bateman, I., Kahneman, D., Munro, A., Starmer, C., & Sugden, R. (2005). Testing competing models of loss aversion: an adversarial collaboration. Journal of Public Economics, 89(8), 1561–1580. https://doi.org/10.1016/j.jpubeco.2004.06.013", + "auto_ref": true + }, + { + "doi": "10.1007/978-3-031-29148-7_32", + "apa": "Clark, C. J., & Tetlock, P. E. (2023). Adversarial Collaboration: The Next Science Reform. Ideological and Political Bias in Psychology, 905–927. https://doi.org/10.1007/978-3-031-29148-7_32", + "auto_ref": true + }, + { + "doi": "10.1177/10892680211015636", + "apa": "Derksen, M., & Field, S. (2021). The Tone Debate: Knowledge, Self, and Social Order. Review of General Psychology, 26(2), 172–183. https://doi.org/10.1177/10892680211015636", + "auto_ref": true + }, + { + "doi": "", + "apa": "Kahneman, D. (2003). Experiences of Collaborative Research. American Psychologist, 58(9), 723–730. https://oce-ovid-com.utrechtuniversity.idm.oclc.org/article/00000487-200309000-00003/HTML", + "auto_ref": false + }, + { + "doi": "10.1038/d41586-025-01379-3", + "apa": "Make science more collegial: why the time for ‘adversarial collaboration’ has come. (2025). Nature, 641(8062), 281–282. https://doi.org/10.1038/d41586-025-01379-3", + "auto_ref": true + }, + { + "doi": "10.1177/1556264614552421", + "apa": "Tijdink, J. K., Verbeke, R., & Smulders, Y. M. (2014). Publication Pressure and Scientific Misconduct in Medical Scientists. Journal of Empirical Research on Human Research Ethics, 9(5), 64–71. https://doi.org/10.1177/1556264614552421", + "auto_ref": true + } + ] + }, + { + "name": "Big team science", + "description": "In big team science (sometimes referred to as “team science”), many researchers pool their resources to solve a problem or answer a research question together, usually resulting in one or several outputs that all researchers involved gain authorship on. Big team science projects can either be coordinated by an organisation (e.g. ManyBabies), or can be run independently by a group of researchers.", + "publications": [ + { + "doi": "10.1186/s13104-022-05944-1", + "apa": "Azevedo, F., Liu, M., Pennington, C. R., Pownall, M., Evans, T. R., Parsons, S., Elsherif, M. M., Micheli, L., & Westwood, S. J. (2022). Towards a culture of open scholarship: the role of pedagogical communities. BMC Research Notes, 15(1). https://doi.org/10.1186/s13104-022-05944-1", + "auto_ref": true + }, + { + "doi": "10.4135/9781529602074", + "apa": "Baum, M., Hart, A., Elsherif, M., Ilchovska, Z., Moreau, D., Dokovova, M., LaPlume, A., Krautter, K., & Staal, J. (2022). Research Without Borders: How to Identify and Overcome Potential Pitfalls in International Large-Team Online Research Projects. SAGE Publications, Ltd. https://doi.org/10.4135/9781529602074", + "auto_ref": true + }, + { + "doi": "10.1098/rsos.230235", + "apa": "Baumgartner, H. A., Alessandroni, N., Byers-Heinlein, K., Frank, M. C., Hamlin, J. K., Soderstrom, M., Voelkel, J. G., Willer, R., Yuen, F., & Coles, N. A. (2023). How to build up big team science: a practical guide for large-scale collaborations. Royal Society Open Science, 10(6). https://doi.org/10.1098/rsos.230235", + "auto_ref": true + }, + { + "doi": "10.1038/s41562-023-01572-2", + "apa": "Coles, N. A., DeBruine, L. M., Azevedo, F., Baumgartner, H. A., & Frank, M. C. (2023). ‘Big team’ science challenges us to reconsider authorship. Nature Human Behaviour, 7(5), 665–667. https://doi.org/10.1038/s41562-023-01572-2", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/rfkyu", + "apa": "Darda, K. M., Conry-Murray, C., Schmidt, K., Elsherif, M. M., Peverill, M., Yoneda, T., Lawson, K. M., DiGregory, E., Moreau, D., Shorter, G. W., & Gernsbacher, M. A. (2023). Promoting Civility in Formal And Informal Open Science Contexts. https://doi.org/10.31234/osf.io/rfkyu", + "auto_ref": true + }, + { + "doi": "10.1126/scitranslmed.3000421", + "apa": "Disis, M. L., & Slattery, J. T. (2010). The Road We Must Take: Multidisciplinary Team Science. Science Translational Medicine, 2(22). https://doi.org/10.1126/scitranslmed.3000421", + "auto_ref": true + }, + { + "doi": "10.1177/17456916221082970", + "apa": "Forscher, P. S., Wagenmakers, E.-J., Coles, N. A., Silan, M. A., Dutra, N., Basnight-Brown, D., & IJzerman, H. (2022). The Benefits, Barriers, and Risks of Big-Team Science. Perspectives on Psychological Science, 18(3), 607–623. https://doi.org/10.1177/17456916221082970", + "auto_ref": true + }, + { + "doi": "", + "apa": "Forscher, P. S., Wagenmakers, E. J., DeBruine, L., Coles, N., Silan, M. A., & IJzerman, H. (2020). A Manifesto for Team Science.", + "auto_ref": false + }, + { + "doi": "10.17605/OSF.IO/WX4ZD", + "apa": "Lakens, D., & Lieck, D. (2022). An Overview of Team Science Projects in the Social Behavioral Sciences. OSF. https://doi.org/10.17605/OSF.IO/WX4ZD", + "auto_ref": true + }, + { + "doi": "10.1038/526189a", + "apa": "Silberzahn, R., & Uhlmann, E. L. (2015). Crowdsourced research: Many hands make tight work. Nature, 526(7572), 189–191. https://doi.org/10.1038/526189a", + "auto_ref": true + }, + { + "doi": "10.3389/fpsyg.2019.00247", + "apa": "Wagge, J. R., Brandt, M. J., Lazarevic, L. B., Legate, N., Christopherson, C., Wiggins, B., & Grahe, J. E. (2019). Publishing Research With Undergraduate Students via Replication Work: The Collaborative Replications and Education Project. Frontiers in Psychology, 10. https://doi.org/10.3389/fpsyg.2019.00247", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pcbi.1010954", + "apa": "Zivony, A., Kardosh, R., Timmins, L., & Reggev, N. (2023). Ten simple rules for socially responsible science. PLOS Computational Biology, 19(3), e1010954. https://doi.org/10.1371/journal.pcbi.1010954", + "auto_ref": true + } + ] + }, + { + "name": "Community science", + "description": "Community science, sometimes called “citizen science”, is scientific research conducted, in whole or in part, by amateur (or non-professional) scientists. Community science is sometimes described as \"public participation in scientific research,\" participatory monitoring, and participatory action research whose outcomes are often advancements in scientific research by improving the scientific community's capacity, as well as increasing the public's understanding of science.", + "publications": [ + { + "doi": "10.1525/bio.2009.59.11.9", + "apa": "Bonney, R., Cooper, C. B., Dickinson, J., Kelling, S., Phillips, T., Rosenberg, K. V., & Shirk, J. (2009). Citizen Science: A Developing Tool for Expanding Science Knowledge and Scientific Literacy. BioScience, 59(11), 977–984. https://doi.org/10.1525/bio.2009.59.11.9", + "auto_ref": true + }, + { + "doi": "10.1126/science.1251554", + "apa": "Bonney, R., Shirk, J. L., Phillips, T. B., Wiggins, A., Ballard, H. L., Miller-Rushing, A. J., & Parrish, J. K. (2014). Next Steps for Citizen Science. Science, 343(6178), 1436–1437. https://doi.org/10.1126/science.1251554", + "auto_ref": true + }, + { + "doi": "10.1641/B580303", + "apa": "Cohn, J. P. (2008). Citizen Science: Can Volunteers Do Real Research? BioScience, 58(3), 192–197. https://doi.org/10.1641/b580303", + "auto_ref": true + }, + { + "doi": "10.1016/j.respol.2013.07.005", + "apa": "Franzoni, C., & Sauermann, H. (2014). Crowd science: The organization of scientific research in open collaborative projects. Research Policy, 43(1), 1–20. https://doi.org/10.1016/j.respol.2013.07.005", + "auto_ref": true + }, + { + "doi": "10.14324/111.9781787352339", + "apa": "Citzen Science. (2018). https://doi.org/10.14324/111.9781787352339", + "auto_ref": true + }, + { + "doi": "", + "apa": "Hart, D.D., and Silka, L. (2020). Rebuilding the Ivory Tower: A Bottom-Up Experiment in Aligning Research with Societal Needs. Issues in Science and Technology, 36(3), 64–70. https://issues.org/aligning-research-with-societal-needs/", + "auto_ref": false + }, + { + "doi": "10.1038/d41586-022-02805-6", + "apa": "Picot, L. E., & Fallon Grasham, C. (2022). Fieldwork: institutions can make it more ethical. Nature, 609(7926), 245–245. https://doi.org/10.1038/d41586-022-02805-6", + "auto_ref": true + }, + { + "doi": "10.3897/rio.9.e96476", + "apa": "Serbe-Kamp, É., Bemme, J., Pollak, D., & Mayer, K. (2023). Open Citizen Science: fostering open knowledge with participation. Research Ideas and Outcomes, 9. https://doi.org/10.3897/rio.9.e96476", + "auto_ref": true + } + ] + }, + { + "name": "Environmental sustainability (e.g. conference travel, high performance computing, etc.)", + "description": "Examines the climate and environmental footprint of research workflows and infrastructures.", + "publications": [ + { + "doi": "10.1080/09644016.2023.2193068", + "apa": "Katz-Rosene, R. M., & Pasek, A. (2023). Spiral-scaling climate action: lessons from and for the academic flying less movement. Environmental Politics, 33(2), 259–280. https://doi.org/10.1080/09644016.2023.2193068", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-020-02057-2", + "apa": "Klöwer, M., Hopkins, D., Allen, M., & Higham, J. (2020). An analysis of ways to decarbonize conference travel after COVID-19. Nature, 583(7816), 356–359. https://doi.org/10.1038/d41586-020-02057-2", + "auto_ref": true + }, + { + "doi": "10.3389/fpsyg.2022.906108", + "apa": "Köhler, J. K., Kreil, A. S., Wenger, A., Darmandieu, A., Graves, C., Haugestad, C. A. P., Holzen, V., Keller, E., Lloyd, S., Marczak, M., Međugorac, V., & Rosa, C. D. (2022). The Need for Sustainability, Equity, and International Exchange: Perspectives of Early Career Environmental Psychologists on the Future of Conferences. Frontiers in Psychology, 13. https://doi.org/10.3389/fpsyg.2022.906108", + "auto_ref": true + }, + { + "doi": "10.1038/s43586-023-00202-5", + "apa": "Lannelongue, L., & Inouye, M. (2023). Carbon footprint estimation for computational research. Nature Reviews Methods Primers, 3(1). https://doi.org/10.1038/s43586-023-00202-5", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0066508", + "apa": "Spinellis, D., & Louridas, P. (2013). The Carbon Footprint of Conference Papers. PLoS ONE, 8(6), e66508. https://doi.org/10.1371/journal.pone.0066508", + "auto_ref": true + }, + { + "doi": "10.1038/s41467-021-27251-2", + "apa": "Tao, Y., Steckel, D., Klemeš, J. J., & You, F. (2021). Trend towards virtual and hybrid conferences may be an effective climate change mitigation strategy. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-27251-2", + "auto_ref": true + } + ] + }, + { + "name": "Participatory research", + "description": "Participatory research, sometimes also referred to as co-production, is an umbrella term for methods in which views and engagement of interested parties from relevant communities (academic or otherwise) are included throughout the research process, from conception to dissemination.", + "publications": [ + { + "doi": "10.1371/journal.pmed.1001089", + "apa": "Boga, M., Davies, A., Kamuya, D., Kinyanjui, S. M., Kivaya, E., Kombe, F., Lang, T., Marsh, V., Mbete, B., Mlamba, A., Molyneux, S., Mulupi, S., & Mwalukore, S. (2011). Strengthening the Informed Consent Process in International Health Research through Community Engagement: The KEMRI-Wellcome Trust Research Programme Experience. PLoS Medicine, 8(9), e1001089. https://doi.org/10.1371/journal.pmed.1001089", + "auto_ref": true + }, + { + "doi": "10.1146/annurev.publhealth.29.091307.083824", + "apa": "Cargo, M., & Mercer, S. L. (2008). The Value and Challenges of Participatory Research: Strengthening Its Practice. Annual Review of Public Health, 29(1), 325–350. https://doi.org/10.1146/annurev.publhealth.29.091307.083824", + "auto_ref": true + }, + { + "doi": "10.1007/s40474-021-00227-z", + "apa": "Fletcher-Watson, S., Brook, K., Hallett, S., Murray, F., & Crompton, C. J. (2021). Inclusive Practices for Neurodevelopmental Research. Current Developmental Disorders Reports, 8(2), 88–97. https://doi.org/10.1007/s40474-021-00227-z", + "auto_ref": true + }, + { + "doi": "10.53841/bpscog.2023.1.8.23", + "apa": "Gourdon-Kanhukamwe, A., Kalandadze, T., Yeung, S. K., Azevedo, F., Iley, B., Phan, J. M., Ramji, A. V., Shaw, J. J., Zaneva, M., Dokovova, M., Hartmann, H., Kapp, S. K., Warrington, K. L., & Elsherif, M. M. (2023). Opening up understanding of neurodiversity: A call for applying participatory and open scholarship practices. The Cognitive Psychology Bulletin, 1(8), 23–27. https://doi.org/10.53841/bpscog.2023.1.8.23", + "auto_ref": true + }, + { + "doi": "10.1177/1556264615592385", + "apa": "Jao, I., Kombe, F., Mwalukore, S., Bull, S., Parker, M., Kamuya, D., Molyneux, S., & Marsh, V. (2015). Involving Research Stakeholders in Developing Policy on Sharing Public Health Research Data in Kenya. Journal of Empirical Research on Human Research Ethics, 10(3), 264–277. https://doi.org/10.1177/1556264615592385", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0135545", + "apa": "Jao, I., Kombe, F., Mwalukore, S., Bull, S., Parker, M., Kamuya, D., Molyneux, S., & Marsh, V. (2015). Research Stakeholders’ Views on Benefits and Challenges for Public Health Research Data Sharing in Kenya: The Importance of Trust and Social Relations. 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Brazilian Journal of Biology, 74(3 suppl 1), s01–s02. https://doi.org/10.1590/1519-6984.03013", + "auto_ref": true + }, + { + "doi": "10.1177/1077800416643994", + "apa": "Ulmer, J. B. (2016). Writing Slow Ontology. Qualitative Inquiry, 23(3), 201–211. https://doi.org/10.1177/1077800416643994", + "auto_ref": true + }, + { + "doi": "10.1177/0961463x13517537", + "apa": "Vostal, F. (2014). Academic life in the fast lane: The experience of time and speed in British academia. Time & Society, 24(1), 71–95. https://doi.org/10.1177/0961463x13517537", + "auto_ref": true + } + ] + }, + { + "name": "Types of academic, non-academic, & alt-academic positions", + "description": "There are many interesting career options beyond academia for those who are currently in the academic system. 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Quality research needs good working conditions. Nature Human Behaviour, 7(2), 164–167. https://doi.org/10.1038/s41562-022-01508-2", + "auto_ref": true + } + ] + } + ] + }, + { + "number": 4, + "name": "Pre-analysis Planning", + "description": "Pre-analysis planning entails laying out a complete methodology and analysis before a study has been undertaken. This facilitates transparency and removes several potential QRPs. When teaching, students should attain knowledge regarding what a pre-registration entails, why it is important to remove potential QRPs and how to address deviations from preregistered plans. There are 5 sub-clusters which aim to further parse the learning and teaching process:", + "sub_clusters": [ + { + "name": "Preregistration", + "description": "When a researcher preregisters their work, they typically upload a detailed project plan before the start of data collection. 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Standard Operating Procedures: A Safety Net for Pre-Analysis Plans. Political Science and Politics, 49(3), 495–500. https://doi.org/10.1017/s1049096516000810", + "auto_ref": true + }, + { + "doi": "10.1027/1864-9335/a000192", + "apa": "Nosek, B. A., & Lakens, D. (2014). Registered Reports. Social Psychology, 45(3), 137–141. https://doi.org/10.1027/1864-9335/a000192", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.1708274114", + "apa": "Nosek, B. A., Ebersole, C. R., DeHaven, A. C., & Mellor, D. T. (2018). The preregistration revolution. Proceedings of the National Academy of Sciences, 115(11), 2600–2606. https://doi.org/10.1073/pnas.1708274114", + "auto_ref": true + }, + { + "doi": "10.1038/526182a", + "apa": "Nuzzo, R. (2015). How scientists fool themselves – and how they can stop. Nature, 526(7572), 182–185. https://doi.org/10.1038/526182a", + "auto_ref": true + }, + { + "doi": "", + "apa": "Wagenmakers, E. J., & Dutilh, G. (2016). Seven selfish reasons for preregistration. APS Observer, 29(9). https://www.psychologicalscience.org/observer/seven-selfish-reasons-for-preregistration", + "auto_ref": false + }, + { + "doi": "10.3389/fpsyg.2016.01832", + "apa": "Wicherts, J. M., Veldkamp, C. L. S., Augusteijn, H. E. M., Bakker, M., van Aert, R. C. M., & van Assen, M. A. L. M. (2016). Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking. Frontiers in Psychology, 7. https://doi.org/10.3389/fpsyg.2016.01832", + "auto_ref": true + } + ] + }, + { + "name": "Registered reports", + "description": "A publishing format consisting of a preregistration with a specific journal that undergoes peer review. Specifically, the journal reviews the introduction and methodology and upon in-principle acceptance (IPA, in stage 1), it agrees to publish the study assuming the preregistration is followed and deviations are reported (stage 2 acceptance).", + "publications": [ + { + "doi": "10.1177/1745691614545653", + "apa": "Alogna, V. K., Attaya, M. K., Aucoin, P., Bahník, Š., Birch, S., Birt, A. R., Bornstein, B. H., Bouwmeester, S., Brandimonte, M. A., Brown, C., Buswell, K., Carlson, C., Carlson, M., Chu, S., Cislak, A., Colarusso, M., Colloff, M. F., Dellapaolera, K. S., Delvenne, J.-F., … Zwaan, R. A. (2014). Registered Replication Report. Perspectives on Psychological Science, 9(5), 556–578. https://doi.org/10.1177/1745691614545653", + "auto_ref": true + }, + { + "doi": "", + "apa": "Anon. (n.d.). Wiley’s Reviewing Registered Reports. https://authorservices.wiley.com/Reviewers/journal-reviewers/how-to-perform-a-peer-review/reviewing-registered-reports.html", + "auto_ref": false + }, + { + "doi": "10.1016/j.cortex.2012.12.016", + "apa": "Chambers, C. D. (2013). Registered Reports: A new publishing initiative at Cortex. Cortex, 49(3), 609–610. https://doi.org/10.1016/j.cortex.2012.12.016", + "auto_ref": true + }, + { + "doi": "10.1016/j.cortex.2015.03.022", + "apa": "Chambers, C. D., Dienes, Z., McIntosh, R. D., Rotshtein, P., & Willmes, K. (2015). Registered Reports: Realigning incentives in scientific publishing. Cortex, 66, A1–A2. https://doi.org/10.1016/j.cortex.2015.03.022", + "auto_ref": true + }, + { + "doi": "10.3934/Neuroscience.2014.1.4", + "apa": "D. Chambers, C., Feredoes, E., D. Muthukumaraswamy, S., & J. Etchells, P. (2014). Instead of “playing the game” it is time to change the rules: Registered Reports at AIMS Neuroscience and beyond. AIMS Neuroscience, 1(1), 4–17. https://doi.org/10.3934/neuroscience.2014.1.4", + "auto_ref": true + }, + { + "doi": "10.1016/j.cortex.2015.03.022", + "apa": "Chambers, C. D., Dienes, Z., McIntosh, R. D., Rotshtein, P., & Willmes, K. (2015). Registered Reports: Realigning incentives in scientific publishing. Cortex, 66, A1–A2. https://doi.org/10.1016/j.cortex.2015.03.022", + "auto_ref": true + }, + { + "doi": "10.1038/s41562-021-01193-7", + "apa": "Chambers, C. D., & Tzavella, L. (2021). The past, present and future of Registered Reports. Nature Human Behaviour, 6(1), 29–42. https://doi.org/10.1038/s41562-021-01193-7", + "auto_ref": true + }, + { + "doi": "10.1002/ece3.10023", + "apa": "Gya, R., Birkeli, K., Dahle, I. J., Foote, C. G., Geange, S. R., Lynn, J. S., Töpper, J. P., Vandvik, V., Zernichow, C., & Jenkins, G. B. (2023). Registered Reports: A new chapter at Ecology & Evolution. Ecology and Evolution, 13(4). Portico. https://doi.org/10.1002/ece3.10023", + "auto_ref": true + }, + { + "doi": "10.1038/s41562-021-01265-8", + "apa": "Karhulahti, V.-M. (2022). Registered reports for qualitative research. Nature Human Behaviour, 6(1), 4–5. https://doi.org/10.1038/s41562-021-01265-8", + "auto_ref": true + }, + { + "doi": "", + "apa": "Zotero. (n.d.). OSF Collection of Registered Reports. Zotero. https://www.zotero.org/groups/479248/osf/collections/KEJP68G9/search/right/titleCreatorYear", + "auto_ref": false + } + ] + }, + { + "name": "Study Design", + "description": "Design elements should be before data collection so that confirmatory claims are credible and deviations are interpretable. This includes choosing appropriate sample sizes, conditions, and measures prior to registration, and planning how to handle deviations", + "publications": [ + { + "doi": "10.31234/osf.io/ha29k", + "apa": "Lakens, D. (2023). When and How to Deviate from a Preregistration. https://doi.org/10.31234/osf.io/ha29k", + "auto_ref": true + } + ] + }, + { + "name": "Understanding the types of preregistration and writing one.", + "description": "Practical materials and resources to move beyond the theory of preregistration, into conducting a preregistered study.", + "publications": [ + { + "doi": "", + "apa": "Call, M., DeHaven, A. C., Pfeiffer, N., Mellor, D. T., & Lowrey, O. (2023, October 19). Templates of OSF registration forms. OSF. https://osf.io/zab38/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Centre for Open Science. (n.d.). Registered Reports: Peer review before results are known to align scientific values and practices. Www.cos.io. https://www.cos.io/initiatives/registered-reports", + "auto_ref": false + }, + { + "doi": "10.31234/osf.io/ha29k", + "apa": "Lakens, D. (2023). When and How to Deviate from a Preregistration. https://doi.org/10.31234/osf.io/ha29k", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/ph4q7", + "apa": "Mertens, G., & Krypotos, A.-M. (2019). Preregistration of analyses of preexisting data. https://doi.org/10.31234/osf.io/ph4q7", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.1708274114", + "apa": "Nosek, B. A., Ebersole, C. R., DeHaven, A. C., & Mellor, D. T. (2018). The preregistration revolution. Proceedings of the National Academy of Sciences, 115(11), 2600–2606. https://doi.org/10.1073/pnas.1708274114", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/8v2n7", + "apa": "Stewart, S. L. K., Rinke, E. M., McGarrigle, R., Lynott, D., Lunny, C., Lautarescu, A., Galizzi, M. M., Farran, E. K., & Crook, Z. (2020). Pre-registration and Registered Reports: a Primer from UKRN. https://doi.org/10.31219/osf.io/8v2n7", + "auto_ref": true + }, + { + "doi": "10.1186/s13643-023-02281-7", + "apa": "van den Akker, O. R., Peters, G.-J. Y., Bakker, C. J., Carlsson, R., Coles, N. A., Corker, K. S., Feldman, G., Moreau, D., Nordström, T., Pickering, J. S., Riegelman, A., Topor, M. K., van Veggel, N., Yeung, S. K., Call, M., Mellor, D. T., & Pfeiffer, N. (2023). Increasing the transparency of systematic reviews: presenting a generalized registration form. Systematic Reviews, 12(1). https://doi.org/10.1186/s13643-023-02281-7", + "auto_ref": true + } + ] + } + ] + }, + { + "number": 5, + "name": "Transparency and reproducibility in computation and analysis", + "description": "Attainment of the how-to basics of reproducible reports and analyses. It requires students to move towards transparent and scripted analysis practices in quantitative research. There are 5 sub-clusters which aim to further parse the learning and teaching process:", + "sub_clusters": [ + { + "name": "Analysis and reporting in qualitative research", + "description": "By documenting and reporting research processes in qualitative research, transparency and credibility in qualitative research reports is ensured. Topics include using agreed reporting standards, demonstrating methodological rigor, and recent calls to integrate qualitative methods into the open science movement. The emphasis is on making qualitative research as trustworthy and open as context permits, without forcing inappropriate replication model", + "publications": [ + { + "doi": "", + "apa": "Anon. (n.d.). OSL Open Stats Lab. Trinity Sites. https://sites.trinity.edu/osl/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Anon. (n.d.). Software carpentry. Software Carpentry. https://software-carpentry.org/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Anon. (n.d.). Teaching integrity in empirical research. Project TIER | Teaching Integrity in Empirical Research. https://www.projecttier.org/", + "auto_ref": false + }, + { + "doi": "10.1080/14780887.2021.1995555", + "apa": "Clarke, V. (2021). Navigating the messy swamp of qualitative research: Are generic reporting standards the answer?A review essay of the book Reporting Qualitative Research in Psychology: How to Meet APA Style Journal Article Reporting Standards, Revised Edition, by Heidi M. Levitt, Washington, DC, American Psychological Association, 2020, 173pp., $29.99 (paperback), ISBN: 978-1-4338-3343-4. Qualitative Research in Psychology, 19(4), 1004–1012. https://doi.org/10.1080/14780887.2021.1995555", + "auto_ref": true + }, + { + "doi": "10.1097/ACM.0000000000000388", + "apa": "O’Brien, B. C., Harris, I. B., Beckman, T. J., Reed, D. A., & Cook, D. A. (2014). Standards for Reporting Qualitative Research. Academic Medicine, 89(9), 1245–1251. https://doi.org/10.1097/acm.0000000000000388", + "auto_ref": true + }, + { + "doi": "10.1093/intqhc/mzm042", + "apa": "Tong, A., Sainsbury, P., & Craig, J. (2007). Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups. International Journal for Quality in Health Care, 19(6), 349–357. https://doi.org/10.1093/intqhc/mzm042", + "auto_ref": true + } + ] + }, + { + "name": "Computational reproducibility", + "description": "Making sure anyone can reproduce quantitative analyses through things like well-commented scripts, writing codebooks, version control, literate programming (e.g. Quarto), reproducible computational environment (containers, package managers), and automated data pipelines.", + "publications": [ + { + "doi": "10.1038/s41567-018-0342-2", + "apa": "Chen, X., Dallmeier-Tiessen, S., Dasler, R., Feger, S., Fokianos, P., Gonzalez, J. B., Hirvonsalo, H., Kousidis, D., Lavasa, A., Mele, S., Rodriguez, D. R., Šimko, T., Smith, T., Trisovic, A., Trzcinska, A., Tsanaktsidis, I., Zimmermann, M., Cranmer, K., Heinrich, L., … Neubert, S. (2018). Open is not enough. Nature Physics, 15(2), 113–119. https://doi.org/10.1038/s41567-018-0342-2", + "auto_ref": true + }, + { + "doi": "10.1207/s15430421tip3903_2", + "apa": "Creswell, J. W., & Miller, D. L. (2000). Determining Validity in Qualitative Inquiry. Theory Into Practice, 39(3), 124–130. https://doi.org/10.1207/s15430421tip3903_2", + "auto_ref": true + }, + { + "doi": "", + "apa": "Data Carpentry. (n.d.). Reproducible research in R workshop overview. https://datacarpentry.org/rr-workshop/", + "auto_ref": false + }, + { + "doi": "10.1177/104973230201200211", + "apa": "Davies, D., & Dodd, J. (2002). Qualitative Research and the Question of Rigor. Qualitative Health Research, 12(2), 279–289. https://doi.org/10.1177/104973230201200211", + "auto_ref": true + }, + { + "doi": "", + "apa": "Fox, N. (2018). Writing reproducible scientific papers in R. YouTube. https://www.youtube.com/playlist?list=PLmvNihjFsoM5hpQdqoI7onL4oXDSQ0ym8", + "auto_ref": false + }, + { + "doi": "10.31235/osf.io/wc35g", + "apa": "Frohwirth, L., Karcher, S., & Lever, T. A. (2023). A Transparency Checklist for Qualitative Research. https://doi.org/10.31235/osf.io/wc35g", + "auto_ref": true + }, + { + "doi": "", + "apa": "Gandrud, C. (2016). Reproducible research with R and R Studio. CRC Press.", + "auto_ref": false + }, + { + "doi": "10.1037/mot0000398", + "apa": "Harmon-Jones, E., Harmon-Jones, C., Amodio, D. M., Gable, P. A., & Schmeichel, B. J. (2025). Valid replications require valid methods: Recommendations for best methodological practices with lab experiments. Motivation Science, 11(3), 235–245. https://doi.org/10.1037/mot0000398", + "auto_ref": true + }, + { + "doi": "", + "apa": "Harrison, P., Barugahare, A., & Tsyganov, K., (2020). Reproducible research in R. Monash Data Fluency. https://monashdatafluency.github.io/r-rep-res/index.html", + "auto_ref": false + }, + { + "doi": "10.1093/joc/jqab026", + "apa": "Humphreys, L., Lewis, N. A., Sender, K., & Won, A. S. (2021). Integrating Qualitative Methods and Open Science: Five Principles for More Trustworthy Research*. Journal of Communication. https://doi.org/10.1093/joc/jqab026", + "auto_ref": true + }, + { + "doi": "10.3897/rio.8.e98457", + "apa": "Ross-Hellauer, T., Klebel, T., Bannach-Brown, A., Horbach, S. P. J. M., Jabeen, H., Manola, N., Metodiev, T., Papageorgiou, H., Reczko, M., Sansone, S.-A., Schneider, J., Tijdink, J., & Vergoulis, T. (2022). TIER2: enhancing Trust, Integrity and Efficiency in Research through next-level Reproducibility. Research Ideas and Outcomes, 8. https://doi.org/10.3897/rio.8.e98457", + "auto_ref": true + }, + { + "doi": "10.3390/clockssleep6010001", + "apa": "Siraji, M. A., & Rahman, M. (2023). Primer on Reproducible Research in R: Enhancing Transparency and Scientific Rigor. Clocks & Sleep, 6(1), 1–10. https://doi.org/10.3390/clockssleep6010001", + "auto_ref": true + }, + { + "doi": "10.5334/jors.ay", + "apa": "Stodden, V., & Miguez, S. (2014). Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research. Journal of Open Research Software, 2(1). https://doi.org/10.5334/jors.ay", + "auto_ref": true + }, + { + "doi": "10.5688/ajpe7120", + "apa": "Johnson, J. L., Adkins, D., & Chauvin, S. (2020). A Review of the Quality Indicators of Rigor in Qualitative Research. American Journal of Pharmaceutical Education, 84(1), 7120. https://doi.org/10.5688/ajpe7120", + "auto_ref": true + }, + { + "doi": "10.1017/S1049096520000955", + "apa": "Kapiszewski, D., & Karcher, S. (2020). Transparency in Practice in Qualitative Research. PS: Political Science & Politics, 54(2), 285–291. https://doi.org/10.1017/s1049096520000955", + "auto_ref": true + }, + { + "doi": "10.1037/amp0000151", + "apa": "Levitt, H. M., Bamberg, M., Creswell, J. W., Frost, D. M., Josselson, R., & Suárez-Orozco, C. (2018). Journal article reporting standards for qualitative primary, qualitative meta-analytic, and mixed methods research in psychology: The APA Publications and Communications Board task force report. American Psychologist, 73(1), 26–46. https://doi.org/10.1037/amp0000151", + "auto_ref": true + }, + { + "doi": "", + "apa": "Levitt, H. M. (2020). Reporting qualitative research in psychology: How to meet APA style journal article reporting standards. American Psychological Association.", + "auto_ref": false + }, + { + "doi": "10.1002/ev.1427", + "apa": "Lincoln, Y. S., & Guba, E. G. (1986). But is it rigorous? Trustworthiness and authenticity in naturalistic evaluation. New Directions for Program Evaluation, 1986(30), 73–84. Portico. https://doi.org/10.1002/ev.1427", + "auto_ref": true + }, + { + "doi": "10.1080/13803611.2021.2022310", + "apa": "Makel, M. C., Meyer, M. S., Simonsen, M. A., Roberts, A. M., & Plucker, J. A. (2022). Replication is relevant to qualitative research. Educational Research and Evaluation, 27(1–2), 215–219. https://doi.org/10.1080/13803611.2021.2022310", + "auto_ref": true + }, + { + "doi": "10.1016/S0140-6736(01)05627-6", + "apa": "Malterud, K. (2001). Qualitative research: standards, challenges, and guidelines. The Lancet, 358(9280), 483–488. https://doi.org/10.1016/s0140-6736(01)05627-6", + "auto_ref": true + }, + { + "doi": "10.1038/s41559-023-02063-3", + "apa": "Merow, C., Serra-Diaz, J. M., Enquist, B. J., & Wilson, A. M. (2023). AI chatbots can boost scientific coding. Nature Ecology & Evolution, 7(7), 960–962. https://doi.org/10.1038/s41559-023-02063-3", + "auto_ref": true + }, + { + "doi": "10.1046/j.1365-2648.2003.02509.x", + "apa": "Mill, J. E., & Ogilvie, L. D. (2003). Establishing methodological rigour in international qualitative nursing research: a case study from Ghana. Journal of Advanced Nursing, 41(1), 80–87. Portico. https://doi.org/10.1046/j.1365-2648.2003.02509.x", + "auto_ref": true + }, + { + "doi": "10.4135/9781526421036", + "apa": "Denzin, Norman. (2020). https://doi.org/10.4135/9781526421036", + "auto_ref": true + }, + { + "doi": "", + "apa": "Navarro, D. (2019, January 11). A tutorial for psychology students and other beginners. (version 0.6.1). Learning Statistics with R. https://learningstatisticswithr.com/book/", + "auto_ref": false + }, + { + "doi": "10.1177/0001839219887663", + "apa": "Pratt, M. G., Kaplan, S., & Whittington, R. (2019). Editorial Essay: The Tumult over Transparency: Decoupling Transparency from Replication in Establishing Trustworthy Qualitative Research. Administrative Science Quarterly, 65(1), 1–19. https://doi.org/10.1177/0001839219887663", + "auto_ref": true + }, + { + "doi": "10.1126/science.1213847", + "apa": "Peng, R. D. (2011). Reproducible Research in Computational Science. Science, 334(6060), 1226–1227. https://doi.org/10.1126/science.1213847", + "auto_ref": true + }, + { + "doi": "", + "apa": "PsyTeachR. (2021). Data Skills for Reproducible Science. PsyTeachR. https://psyteachr.github.io/msc-data-skills/", + "auto_ref": false + }, + { + "doi": "10.1177/1473325017700701", + "apa": "Ruggiano, N., & Perry, T. E. (2017). Conducting secondary analysis of qualitative data: Should we, can we, and how? Qualitative Social Work, 18(1), 81–97. https://doi.org/10.1177/1473325017700701", + "auto_ref": true + }, + { + "doi": "10.1111/bjhp.12393", + "apa": "Shaw, R. L., Bishop, F. L., Horwood, J., Chilcot, J., & Arden, M. A. (2019). Enhancing the quality and transparency of qualitative research methods in health psychology. British Journal of Health Psychology, 24(4), 739–745. Portico. https://doi.org/10.1111/bjhp.12393", + "auto_ref": true + }, + { + "doi": "", + "apa": "Stahl, N. A., & King, J. R. (2020). Expanding approaches for research: Understanding and using trustworthiness in qualitative research. Journal of Developmental Education, 44(1), 26–28. https://files.eric.ed.gov/fulltext/EJ1320570.pdf", + "auto_ref": false + }, + { + "doi": "10.36850/mr7", + "apa": "Steltenpohl, C. N., Lustick, H., Meyer, M. S., Lee, L. E., Stegenga, S. M., Standiford Reyes, L., & Renbarger, R. L. (2023). Rethinking Transparency and Rigor from a Qualitative Open Science Perspective. Journal of Trial and Error, 4(1), 47–59. KB. https://doi.org/10.36850/mr7", + "auto_ref": true + }, + { + "doi": "", + "apa": "Stodden, V., Miguez, S. (2014). Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research. Journal of Open Research Software (1), e21. https://openresearchsoftware.metajnl.com/articles/10.5334/jors.ay", + "auto_ref": false + }, + { + "doi": "10.1080/2159676X.2021.1901138", + "apa": "Tamminen, K. A., Bundon, A., Smith, B., McDonough, M. H., Poucher, Z. A., & Atkinson, M. (2021). Considerations for making informed choices about engaging in open qualitative research. Qualitative Research in Sport, Exercise and Health, 13(5), 864–886. https://doi.org/10.1080/2159676x.2021.1901138", + "auto_ref": true + }, + { + "doi": "10.5281/zenodo.3233986", + "apa": "Community, T. T. W., Arnold, B., Bowler, L., Gibson, S., Herterich, P., Higman, R., Krystalli, A., Morley, A., O'Reilly, M., & Whitaker, K. (2019). The Turing Way: A Handbook for Reproducible Data Science (Version v0.0.4) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.3233986", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pcbi.1005510", + "apa": "Wilson, G., Bryan, J., Cranston, K., Kitzes, J., Nederbragt, L., & Teal, T. K. (2017). Good enough practices in scientific computing. PLOS Computational Biology, 13(6), e1005510. https://doi.org/10.1371/journal.pcbi.1005510", + "auto_ref": true + } + ] + }, + { + "name": "Free and open source software", + "description": "Free and open source software is a foundation for reproducible research: open tooling lowers access barriers, enables community review, and supports longevity through transparent code, issue tracking, and forking.", + "publications": [ + { + "doi": "", + "apa": "Chao, L. (2009). Utilizing open source tools for online teaching and learning Information Science. Information Science Reference.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Huang, R. (2016). RQDA: R-based qualitative data analysis (Version 0.2-8) [Computer software]. R Project. http://rqda.r-forge.r-project.org/", + "auto_ref": false + }, + { + "doi": "10.1371/journal.pcbi.1002598", + "apa": "Morin, A., Urban, J., & Sliz, P. (2012). A Quick Guide to Software Licensing for the Scientist-Programmer. PLoS Computational Biology, 8(7), e1002598. https://doi.org/10.1371/journal.pcbi.1002598", + "auto_ref": true + }, + { + "doi": "10.1002/pds.5815", + "apa": "Nab, L., Schaffer, A. L., Hulme, W., DeVito, N. J., Dillingham, I., Wiedemann, M., Andrews, C. D., Curtis, H., Fisher, L., Green, A., Massey, J., Walters, C. E., Higgins, R., Cunningham, C., Morley, J., Mehrkar, A., Hart, L., Davy, S., Evans, D., … Goldacre, B. (2024). OpenSAFELY: A platform for analysing electronic health records designed for reproducible research. Pharmacoepidemiology and Drug Safety, 33(6). Portico. https://doi.org/10.1002/pds.5815", + "auto_ref": true + }, + { + "doi": "10.1007/s12130-999-1026-0", + "apa": "Raymond, E. (1999). The cathedral and the bazaar. Knowledge, Technology & Policy, 12(3), 23–49. https://doi.org/10.1007/s12130-999-1026-0", + "auto_ref": true + } + ] + }, + { + "name": "Research software engineering", + "description": "Covers the emerging role of Research Software Engineers, professionals who develop software for research purposes. Emphasizes best practices in coding (testing, version control, documentation) as integral to research transparency. Also discusses how RSEs bridge the gap between traditional IT and academic science, ensuring that scientific software is reliable and sustainable", + "publications": [ + { + "doi": "10.7717/peerj-cs.963", + "apa": "Carver, J. C., Weber, N., Ram, K., Gesing, S., & Katz, D. S. (2022). A survey of the state of the practice for research software in the United States. PeerJ Computer Science, 8, e963. Portico. https://doi.org/10.7717/peerj-cs.963", + "auto_ref": true + }, + { + "doi": "10.3233/DS-190026", + "apa": "Lamprecht, A.-L., Garcia, L., Kuzak, M., Martinez, C., Arcila, R., Martin Del Pico, E., Dominguez Del Angel, V., van de Sandt, S., Ison, J., Martinez, P. A., McQuilton, P., Valencia, A., Harrow, J., Psomopoulos, F., Gelpi, J. Ll., Chue Hong, N., Goble, C., & Capella-Gutierrez, S. (2019). Towards FAIR principles for research software. Data Science, 3(1), 37–59. https://doi.org/10.3233/ds-190026", + "auto_ref": true + } + ] + }, + { + "name": "Tools to check yourself and others", + "description": "Detecting errors in the literature, and preventing them from entering the literature by checking your own work. Includes tools such as statcheck.io, GRIM, and SPRITE to detect errors in reporting of statistics.", + "publications": [ + { + "doi": "10.1177/1948550616673876", + "apa": "Brown, N. J. L., & Heathers, J. A. J. (2016). The GRIM Test. Social Psychological and Personality Science, 8(4), 363–369. https://doi.org/10.1177/1948550616673876", + "auto_ref": true + }, + { + "doi": "10.1038/529456a", + "apa": "Baker, M. (2016). How quality control could save your science. Nature, 529(7587), 456–458. https://doi.org/10.1038/529456a", + "auto_ref": true + }, + { + "doi": "", + "apa": "Nuijten, M. B., Van Assen, M. A. L. M., Hartgerink, C. H. J., Epskamp, S., & Wicherts, J. M. (2017). The validity of the tool “statcheck” in discovering statistical reporting inconsistencies. https://psyarxiv.com/tcxaj/.", + "auto_ref": false + }, + { + "doi": "10.1002/cpz1.70299", + "apa": "Pejdo, D., Ursić, L., & Marušić, A. (2025). Primer on Reproducibility: Trends, Tools, and Some Tips and Tricks. Current Protocols, 6(1). Portico. https://doi.org/10.1002/cpz1.70299", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/rsn5y", + "apa": "Strand, J. F. (2021). Error Tight: Exercises for Lab Groups to Prevent Research Mistakes. https://doi.org/10.31234/osf.io/rsn5y", + "auto_ref": true + }, + { + "doi": "10.1186/s40795-017-0167-x", + "apa": "van der Zee, T., Anaya, J., & Brown, N. J. L. (2017). Statistical heartburn: an attempt to digest four pizza publications from the Cornell Food and Brand Lab. BMC Nutrition, 3(1). https://doi.org/10.1186/s40795-017-0167-x", + "auto_ref": true + } + ] + } + ] + }, + { + "number": 6, + "name": "FAIR data and materials", + "description": "Students will learn about FAIR data (and education/research materials) principles that address Findability, Accessibility, Interoperability, and Reusability; engage with reasons to share data, the initiatives designed to increase scientific openness; as well as of possible privacy and security considerations together with anonymization procedures. There are 7 sub-clusters which aim to further parse the learning and teaching process:", + "sub_clusters": [ + { + "name": "Reasons to share data and materials", + "description": "Sharing data and research materials is beneficial for science and society. Open data can enable validation of results, inspire new discoveries through re-use, increase researcher credit (e.g., via data citations), and promote transparency that enhances trust. Key studies have shown that papers with shared data receive more citations and foster broader collaboration.", + "publications": [ + { + "doi": "10.1177/2158244016685136", + "apa": "Bishop, L., & Kuula-Luumi, A. (2017). Revisiting Qualitative Data Reuse. Sage Open, 7(1). https://doi.org/10.1177/2158244016685136", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0230416", + "apa": "Colavizza, G., Hrynaszkiewicz, I., Staden, I., Whitaker, K., & McGillivray, B. (2020). The citation advantage of linking publications to research data. PLOS ONE, 15(4), e0230416. https://doi.org/10.1371/journal.pone.0230416", + "auto_ref": true + }, + { + "doi": "10.1093/joc/jqz052", + "apa": "Dienlin, T., Johannes, N., Bowman, N. D., Masur, P. K., Engesser, S., Kümpel, A. S., Lukito, J., Bier, L. M., Zhang, R., Johnson, B. K., Huskey, R., Schneider, F. M., Breuer, J., Parry, D. A., Vermeulen, I., Fisher, J. T., Banks, J., Weber, R., Ellis, D. A., … de Vreese, C. (2020). An Agenda for Open Science in Communication. Journal of Communication, 71(1), 1–26. https://doi.org/10.1093/joc/jqz052", + "auto_ref": true + }, + { + "doi": "10.1037%2Fqup0000076", + "apa": "DuBois, J. M., Strait, M., & Walsh, H. (2018). Is it time to share qualitative research data? Qualitative Psychology, 5(3), 380–393. https://doi.org/10.1037/qup0000076", + "auto_ref": true + }, + { + "doi": "10.1177/2515245918810225", + "apa": "Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., Aveyard, M., Axt, J. R., Babalola, M. 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Advances in Methods and Practices in Psychological Science, 1(1), 95–103. https://doi.org/10.1177/2515245918758319", + "auto_ref": true + }, + { + "doi": "10.18352/lq.10113", + "apa": "Transparency: The Emerging Third Dimension of Open Science and Open Data. (2016). LIBER QUARTERLY, 25(4), 153–171. https://doi.org/10.18352/lq.10113", + "auto_ref": true + }, + { + "doi": "10.7554/eLife.16800", + "apa": "McKiernan, E. C., Bourne, P. E., Brown, C. T., Buck, S., Kenall, A., Lin, J., McDougall, D., Nosek, B. A., Ram, K., Soderberg, C. K., Spies, J. R., Thaney, K., Updegrove, A., Woo, K. H., & Yarkoni, T. (2016). How open science helps researchers succeed. ELife, 5. CLOCKSS. https://doi.org/10.7554/elife.16800", + "auto_ref": true + }, + { + "doi": "10.1111/j.1740-9713.2015.00827.x", + "apa": "Peng, R. (2015). The Reproducibility Crisis in Science: A Statistical Counterattack. 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Nature Ecology & Evolution, 7(10), 1547–1551. https://doi.org/10.1038/s41559-023-02161-2", + "auto_ref": true + }, + { + "doi": "10.1017/S1537592720001164", + "apa": "Jacobs, A. M., Büthe, T., Arjona, A., Arriola, L. R., Bellin, E., Bennett, A., Björkman, L., Bleich, E., Elkins, Z., Fairfield, T., Gaikwad, N., Greitens, S. C., Hawkesworth, M., Herrera, V., Herrera, Y. M., Johnson, K. S., Karakoç, E., Koivu, K., Kreuzer, M., … Yashar, D. J. (2021). The Qualitative Transparency Deliberations: Insights and Implications. Perspectives on Politics, 19(1), 171–208. https://doi.org/10.1017/s1537592720001164", + "auto_ref": true + }, + { + "doi": "10.1177/1556264615592385", + "apa": "Jao, I., Kombe, F., Mwalukore, S., Bull, S., Parker, M., Kamuya, D., Molyneux, S., & Marsh, V. (2015). Involving Research Stakeholders in Developing Policy on Sharing Public Health Research Data in Kenya. Journal of Empirical Research on Human Research Ethics, 10(3), 264–277. https://doi.org/10.1177/1556264615592385", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0135545", + "apa": "Jao, I., Kombe, F., Mwalukore, S., Bull, S., Parker, M., Kamuya, D., Molyneux, S., & Marsh, V. (2015). Research Stakeholders’ Views on Benefits and Challenges for Public Health Research Data Sharing in Kenya: The Importance of Trust and Social Relations. PLOS ONE, 10(9), e0135545. https://doi.org/10.1371/journal.pone.0135545", + "auto_ref": true + }, + { + "doi": "10.1177/2515245917744281", + "apa": "Joel, S., Eastwick, P. W., & Finkel, E. J. (2018). Open Sharing of Data on Close Relationships and Other Sensitive Social Psychological Topics: Challenges, Tools, and Future Directions. Advances in Methods and Practices in Psychological Science, 1(1), 86–94. https://doi.org/10.1177/2515245917744281", + "auto_ref": true + }, + { + "doi": "10.3389/fsoc.2024.1308029", + "apa": "Khan, S., Hirsch, J. 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Journal of Health Psychology, 29(7), 653–658. https://doi.org/10.1177/13591053231225903", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/5yw4z", + "apa": "Prosser, A. M. B., Hamshaw, R., Meyer, J., Bagnall, R., Blackwood, L., Huysamen, M., Jordan, A., Vasileiou, K., & Walter, Z. (2021). When open data closes the door: A critical examination of the past, present and the potential future for open data guidelines in journals. https://doi.org/10.31234/osf.io/5yw4z", + "auto_ref": true + }, + { + "doi": "10.1037/amp0000240", + "apa": "Ross, M. W., Iguchi, M. Y., & Panicker, S. (2018). Ethical aspects of data sharing and research participant protections. American Psychologist, 73(2), 138–145. https://doi.org/10.1037/amp0000240", + "auto_ref": true + }, + { + "doi": "10.7717/peerj.4269", + "apa": "Siler, K., Haustein, S., Smith, E., Larivière, V., & Alperin, J. P. (2018). Authorial and institutional stratification in open access publishing: the case of global health research. PeerJ, 6, e4269. Portico. https://doi.org/10.7717/peerj.4269", + "auto_ref": true + }, + { + "doi": "10.1016/j.jbi.2022.104257", + "apa": "Strech, D., Haven, T., Madai, V. I., Meurers, T., & Prasser, F. (2023). Generating evidence on privacy outcomes to inform privacy risk management: A way forward? Journal of Biomedical Informatics, 137, 104257. https://doi.org/10.1016/j.jbi.2022.104257", + "auto_ref": true + }, + { + "doi": "10.1177/10497323211054058", + "apa": "VandeVusse, A., Mueller, J., & Karcher, S. (2021). Qualitative Data Sharing: Participant Understanding, Motivation, and Consent. Qualitative Health Research, 32(1), 182–191. https://doi.org/10.1177/10497323211054058", + "auto_ref": true + }, + { + "doi": "10.12688/wellcomeopenres.15480.1", + "apa": "Vaz, M., Palmero, A. G., Nyangulu, W., Diallo, A. A., & Ho, C. W. L. (2019). Diffusion of ethical governance policy on sharing of biological materials and related data for biomedical research. 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C., Cemalcilar, Z., Chandler, J., Cheong, W., Davis, W. E., Devos, T., Eisner, M., Frankowska, N., Furrow, D., Galliani, E. M., … Nosek, B. A. (2014). Investigating Variation in Replicability. Social Psychology, 45(3), 142–152. https://doi.org/10.1027/1864-9335/a000178", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0261719", + "apa": "Mozersky, J., McIntosh, T., Walsh, H. A., Parsons, M. V., Goodman, M., & DuBois, J. M. (2021). Barriers and facilitators to qualitative data sharing in the United States: A survey of qualitative researchers. PLOS ONE, 16(12), e0261719. https://doi.org/10.1371/journal.pone.0261719", + "auto_ref": true + }, + { + "doi": "10.1109/MCSE.2009.19", + "apa": "Stodden, V. (2009). The Legal Framework for Reproducible Scientific Research: Licensing and Copyright. Computing in Science & Engineering, 11(1), 35–40. https://doi.org/10.1109/mcse.2009.19", + "auto_ref": true + }, + { + "doi": "10.1037/0003-066X.61.7.726", + "apa": "Wicherts, J. 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Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02166-3", + "auto_ref": true + }, + { + "doi": "10.1038/sdata.2016.18", + "apa": "Wilkinson, M. D., Dumontier, M., Aalbersberg, Ij. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3(1). https://doi.org/10.1038/sdata.2016.18", + "auto_ref": true + } + ] + }, + { + "name": "Repositories", + "description": "Trusted places to deposit datasets, code, and teaching materials so they remain findable, citable, and preserved.", + "publications": [ + { + "doi": "", + "apa": "Anon. (2019). Home. Open Science Framework. https://osf.io/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Anon. (n.d.). Figshare - credit for all your research. 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Portico. https://doi.org/10.1002/ijc.33882", + "auto_ref": true + }, + { + "doi": "10.46743/2160-3715/2021.5012", + "apa": "Karcher, S., Kirilova, D., Pagé, C., & Weber, N. (2021). How Data Curation Enables Epistemically Responsible Reuse of Qualitative Data. The Qualitative Report. https://doi.org/10.46743/2160-3715/2021.5012", + "auto_ref": true + }, + { + "doi": "10.1177/0002764218784991", + "apa": "Mannheimer, S., Pienta, A., Kirilova, D., Elman, C., & Wutich, A. (2018). Qualitative Data Sharing: Data Repositories and Academic Libraries as Key Partners in Addressing Challenges. American Behavioral Scientist, 63(5), 643–664. https://doi.org/10.1177/0002764218784991", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pcbi.1004525", + "apa": "Michener, W. K. (2015). Ten Simple Rules for Creating a Good Data Management Plan. 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Advances in Methods and Practices in Psychological Science, 8(2), 25152459251336130. https://doi.org/10.1177/251524592513361", + "auto_ref": false + } + ] + }, + { + "name": "FAIR principles applied to Education & Training", + "description": "FAIR isn’t only for datasets, syllabi, slides, and assignments can be findable, accessible, interoperable, and reusable too. This section offers institutional and practical roadmaps to make FAIR-by-design teaching materials the default.", + "publications": [ + { + "doi": "10.5281/zenodo.8305540", + "apa": "Filiposka, S., Green, D., Mishev, A., Kjorveziroski, V., Corleto, A., Napolitano, E., Paolini, G., Di Giorgio, S., Janik, J., Schirru, L., Gingold, A., Hadrossek, C., Souyioultzoglou, I., Leister, C., Pavone, G., Sharma, S., Mendez Rodriguez, E. M., & Lazzeri, E. (2023). D2.2 Methodology for FAIR-by-Design Training Materials. https://doi.org/10.5281/ZENODO.8305540", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pcbi.1013208", + "apa": "Funk, E. M., Toelch, U., Ludwig, R., & Kniffert, S. (2025). Ten quick tips for navigating intellectual property in FAIR educational resources. PLOS Computational Biology, 21(7), e1013208. https://doi.org/10.1371/journal.pcbi.1013208", + "auto_ref": true + }, + { + "doi": "10.7554/eLife.89736", + "apa": "Kohrs, F. E., Auer, S., Bannach-Brown, A., Fiedler, S., Haven, T. L., Heise, V., Holman, C., Azevedo, F., Bernard, R., Bleier, A., Bössel, N., Cahill, B. P., Castro, L. J., Ehrenhofer, A., Eichel, K., Frank, M., Frick, C., Friese, M., Gärtner, A., … Weissgerber, T. L. (2023). Eleven strategies for making reproducible research and open science training the norm at research institutions. ELife, 12. CLOCKSS. https://doi.org/10.7554/elife.89736", + "auto_ref": true + }, + { + "doi": "10.3389/feduc.2024.1390444", + "apa": "Provost, L., Bezuidenhout, L., Venkataraman, S., van der Lek, I., van Gelder, C., Kuchma, I., Leenarts, E., Azevedo, F., Brvar, I. V., Paladin, L., Clare, H., & Braukmann, R. (2024). Towards FAIRification of learning resources and catalogues—lessons learnt from research communities. Frontiers in Education, 9. https://doi.org/10.3389/feduc.2024.1390444", + "auto_ref": true + } + ] + } + ] + }, + { + "number": 7, + "name": "Publication Sharing", + "description": "This cluster has 6 sub-clusters:", + "sub_clusters": [ + { + "name": "Why open access?", + "description": "Open access accelerates knowledge circulation, enables global access and increases visibility and reuse.", + "publications": [ + { + "doi": "10.1038/s41562-023-01637-2", + "apa": "Ahmed, A., Al-Khatib, A., Boum, Y., Debat, H., Gurmendi Dunkelberg, A., Hinchliffe, L. J., Jarrad, F., Mastroianni, A., Mineault, P., Pennington, C. R., & Pruszynski, J. A. (2023). The future of academic publishing. Nature Human Behaviour, 7(7), 1021–1026. https://doi.org/10.1038/s41562-023-01637-2", + "auto_ref": true + }, + { + "doi": "10.7551/mitpress/9286.001.0001", + "apa": "Suber, P. (2012). Open Access. The MIT Press. https://doi.org/10.7551/mitpress/9286.001.0001", + "auto_ref": true + }, + { + "doi": "10.12688/f1000research.8460.3", + "apa": "Tennant, J. P., Waldner, F., Jacques, D. C., Masuzzo, P., Collister, L. B., & Hartgerink, Chris. H. J. (2016). The academic, economic and societal impacts of Open Access: an evidence-based review. F1000Research, 5, 632. https://doi.org/10.12688/f1000research.8460.3", + "auto_ref": true + }, + { + "doi": "", + "apa": "Willinsky, J. (2006). The access principle : the case for open access to research and scholarship. 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Royal Society Open Science, 5(8), 180448. https://doi.org/10.1098/rsos.180448", + "auto_ref": true + }, + { + "doi": "10.3758/s13428-015-0630-z", + "apa": "Rouder, J. N. (2015). The what, why, and how of born-open data. Behavior Research Methods, 48(3), 1062–1069. https://doi.org/10.3758/s13428-015-0630-z", + "auto_ref": true + }, + { + "doi": "10.7717/peerj.4269", + "apa": "Siler, K., Haustein, S., Smith, E., Larivière, V., & Alperin, J. P. (2018). Authorial and institutional stratification in open access publishing: the case of global health research. PeerJ, 6, e4269. Portico. https://doi.org/10.7717/peerj.4269", + "auto_ref": true + }, + { + "doi": "10.7717/peerj.4375", + "apa": "Piwowar, H., Priem, J., Larivière, V., Alperin, J. P., Matthias, L., Norlander, B., Farley, A., West, J., & Haustein, S. (2018). The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles. PeerJ, 6, e4375. Portico. https://doi.org/10.7717/peerj.4375", + "auto_ref": true + } + ] + }, + { + "name": "Open peer review", + "description": "Open peer review typically refers to sharing reviewer reports and/or reviewers signing reviews. It is important to understand which definition is being used to understand the pros and cons.", + "publications": [ + { + "doi": "", + "apa": "Anon. (n.d.). About Meta-Psychology. Meta-Psychology. https://open.lnu.se/index.php/metapsychology/about", + "auto_ref": false + }, + { + "doi": "", + "apa": "Carlsson, R., Lakens, D., van Assen, M.A.L.M., Heene, M., Innes-Ker, A., Schönbrodt, F., Danielsson, H., DeBruine, L., Buchanan, E.M., Kalmendal, A., Holcombe A.O., & Batinovic, L. (2023, March 14). Meta-psychology. OSF. https://osf.io/3m4z3/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Ford, E. (2013). Defining and Characterizing Open Peer Review: A Review of the Literature. Journal of Scholarly Publishing 44(4), 311-326. https://muse.jhu.edu/article/513250.", + "auto_ref": false + }, + { + "doi": "10.1186/s13059-020-02004-4", + "apa": "Halffman, W., & Horbach, S. P. J. M. (2020). What are innovations in peer review and editorial assessment for? Genome Biology, 21(1). https://doi.org/10.1186/s13059-020-02004-4", + "auto_ref": true + }, + { + "doi": "10.4337/9781035300174.00015", + "apa": "Halffman, W., & Horbach, S. P. J. M. (2024). Designing journal peer review: diverse expectations, procedures and concerns. How to Edit and Manage a Successful Scholarly Journal, 68–78. https://doi.org/10.4337/9781035300174.00015", + "auto_ref": true + }, + { + "doi": "10.1186/s41073-018-0051-5", + "apa": "Horbach, S. P. J. M., & Halffman, W. ( W. (2018). The changing forms and expectations of peer review. 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Impact of Social Sciences (LSE). https://blogs.lse.ac.uk/impactofsocialsciences/2021/02/10/how-the-pandemic-changed-editorial-peer-review-and-why-we-should-wonder-whether-thats-desirable/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Horbach, S. P. J. M., Ochsner, M., & Kaltenbrunner, W. (2022). Reflections on guest editing a Frontiers journal [Blog post]. Leiden Madtrics. https://www.leidenmadtrics.nl/articles/reflections-on-guest-editing-a-frontiers-journal?", + "auto_ref": false + }, + { + "doi": "", + "apa": "Horbach, S. P. J. M., Ross-Hellauer, T., & Waltman, L. (2022). Sunlight not shadows: Double-anonymized peer review is not the progressive answer to status bias. OSF https://osf.io/preprints/osf/fqb5c_v1", + "auto_ref": false + }, + { + "doi": "10.1016/j.joi.2025.101760", + "apa": "Álvarez-García, E., García-Costa, D., Squazzoni, F., Malički, M., Mehmani, B., & Grimaldo, F. (2026). Published peer review reports have higher informative content than unpublished reports. Journal of Informetrics, 20(1), 101760. https://doi.org/10.1016/j.joi.2025.101760", + "auto_ref": true + }, + { + "doi": "10.1037/abn0000426", + "apa": "Lynam, D. R., Hyatt, C. S., Hopwood, C. J., Wright, A. G. C., & Miller, J. D. (2019). Should psychologists sign their reviews? Some thoughts and some data. Journal of Abnormal Psychology, 128(6), 541–546. https://doi.org/10.1037/abn0000426", + "auto_ref": true + }, + { + "doi": "10.1007/BF01173636", + "apa": "Mahoney, M. J. (1977). Publication prejudices: An experimental study of confirmatory bias in the peer review system. Cognitive Therapy and Research, 1(2), 161–175. https://doi.org/10.1007/bf01173636", + "auto_ref": true + }, + { + "doi": "10.1098/rsos.150547", + "apa": "Morey, R. D., Chambers, C. D., Etchells, P. J., Harris, C. R., Hoekstra, R., Lakens, D., Lewandowsky, S., Morey, C. C., Newman, D. P., Schönbrodt, F. D., Vanpaemel, W., Wagenmakers, E.-J., & Zwaan, R. A. (2016). The Peer Reviewers’ Openness Initiative: incentivizing open research practices through peer review. Royal Society Open Science, 3(1), 150547. https://doi.org/10.1098/rsos.150547", + "auto_ref": true + }, + { + "doi": "10.1001/jama.2016.11014", + "apa": "Okike, K., Hug, K. T., Kocher, M. S., & Leopold, S. S. (2016). Single-blind vs Double-blind Peer Review in the Setting of Author Prestige. JAMA, 316(12), 1315. https://doi.org/10.1001/jama.2016.11014", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pbio.3002255", + "apa": "Ross-Hellauer, T., Bouter, L. M., & Horbach, S. P. J. M. (2023). Open peer review urgently requires evidence: A call to action. PLOS Biology, 21(10), e3002255. https://doi.org/10.1371/journal.pbio.3002255", + "auto_ref": true + }, + { + "doi": "10.1093/reseval/rvae004", + "apa": "Ross-Hellauer, T., & Horbach, S. P. J. M. (2024). Additional experiments required: A scoping review of recent evidence on key aspects of Open Peer Review. Research Evaluation, 33. https://doi.org/10.1093/reseval/rvae004", + "auto_ref": true + }, + { + "doi": "10.12688/f1000research.11369.2", + "apa": "Ross-Hellauer, T. (2017). What is open peer review? A systematic review. F1000Research, 6, 588. https://doi.org/10.12688/f1000research.11369.2", + "auto_ref": true + }, + { + "doi": "10.12688/f1000research.15334.1", + "apa": "Schmidt, B., Ross-Hellauer, T., van Edig, X., & Moylan, E. C. (2018). Ten considerations for open peer review. F1000Research, 7, 969. https://doi.org/10.12688/f1000research.15334.1", + "auto_ref": true + }, + { + "doi": "10.1097/AOG.0000000000003260", + "apa": "Tvina, A., Spellecy, R., & Palatnik, A. (2019). Bias in the Peer Review Process. Obstetrics & Gynecology, 133(6), 1081–1083. https://doi.org/10.1097/aog.0000000000003260", + "auto_ref": true + }, + { + "doi": "10.1136/bmj.318.7175.23", + "apa": "van Rooyen, S., Godlee, F., Evans, S., Black, N., & Smith, R. (1999). Effect of open peer review on quality of reviews and on reviewers’recommendations: a randomised trial. BMJ, 318(7175), 23–27. https://doi.org/10.1136/bmj.318.7175.23", + "auto_ref": true + } + ] + }, + { + "name": "Preprints and postprints", + "description": "To circumvent paywalls and inaccessible scientific work, pre- and postprints can be published on open repositories in order to make the work accessible to all.", + "publications": [ + { + "doi": "", + "apa": "Anon. (n.d.). What are the differences between preprint and postprint versions?. ZB MED - Informationszentrum Lebenswissenschaften. https://www.publisso.de/en/advice/publishing-advice-faqs/preprint-and-postprint", + "auto_ref": false + }, + { + "doi": "10.5281/zenodo.3357727", + "apa": "Chiarelli, A., Johnson, R., Pinfield, S., & Richens, E. (2019). Accelerating scholarly communication: The transformative role of preprints. Zenodo. https://doi.org/10.5281/ZENODO.3357727", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pmed.1002549", + "apa": "Johansson, M. A., Reich, N. G., Meyers, L. A., & Lipsitch, M. (2018). Preprints: An underutilized mechanism to accelerate outbreak science. PLOS Medicine, 15(4), e1002549. https://doi.org/10.1371/journal.pmed.1002549", + "auto_ref": true + } + ] + }, + { + "name": "Rights retention strategies", + "description": "To whom does the paper belong?", + "publications": [ + { + "doi": "", + "apa": "Anon. (n.d.). Plan S rights retention strategy. Plan S. https://www.coalition-s.org/rights-retention-strategy", + "auto_ref": false + } + ] + }, + { + "name": "SPARC Europe - Rights Retention Helper:", + "description": "", + "publications": [ + { + "doi": "", + "apa": "https://sparceurope.org/what-we-do/open-access/copyright/project-retain/rights-retention-helper/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Suber, Peter. 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Pre-replication: anything goes, once. https://doi.org/10.31234/osf.io/5gn7m", + "auto_ref": true + }, + { + "doi": "", + "apa": "King, G. (1995). Replication, replication. PS: Political Science & Politics, 28(3), 444-452. https://gking.harvard.edu/files/replication.pdf", + "auto_ref": false + }, + { + "doi": "10.1017/psa.2023.157", + "apa": "Lavelle, J. S. (2023). Growth From Uncertainty: Understanding the Replication ‘Crisis’ in Infant Cognition. Philosophy of Science, 91(2), 390–409. https://doi.org/10.1017/psa.2023.157", + "auto_ref": true + }, + { + "doi": "", + "apa": "Lenne & Mann (2016). CREP project report. https://osf.io/sdj7e/", + "auto_ref": false + }, + { + "doi": "10.31222/osf.io/jfbr8_v1", + "apa": "McIntosh, B., Ichikawa, K., & Nelson, N. C. (2025). Adversarial reanalysis and the challenge of open data in regulatory science. https://doi.org/10.31222/osf.io/jfbr8_v1", + "auto_ref": true + }, + { + "doi": "10.1177/0001839219887663", + "apa": "Pratt, M. G., Kaplan, S., & Whittington, R. (2019). Editorial Essay: The Tumult over Transparency: Decoupling Transparency from Replication in Establishing Trustworthy Qualitative Research. Administrative Science Quarterly, 65(1), 1–19. https://doi.org/10.1177/0001839219887663", + "auto_ref": true + }, + { + "doi": "10.3897/rio.8.e98457", + "apa": "Ross-Hellauer, T., Klebel, T., Bannach-Brown, A., Horbach, S. P. J. M., Jabeen, H., Manola, N., Metodiev, T., Papageorgiou, H., Reczko, M., Sansone, S.-A., Schneider, J., Tijdink, J., & Vergoulis, T. (2022). TIER2: enhancing Trust, Integrity and Efficiency in Research through next-level Reproducibility. Research Ideas and Outcomes, 8. https://doi.org/10.3897/rio.8.e98457", + "auto_ref": true + }, + { + "doi": "10.1177/1745691614528518", + "apa": "Stanley, D. J., & Spence, J. R. (2014). Expectations for Replications. 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A., Stanley, T. D., & Doucouliagos, H. (2017). The Power of Bias in Economics Research. The Economic Journal, 127(605), F236–F265. https://doi.org/10.1111/ecoj.12461", + "auto_ref": true + }, + { + "doi": "10.1002/jrsm.1663", + "apa": "Ivimey‐Cook, E. R., Noble, D. W. A., Nakagawa, S., Lajeunesse, M. J., & Pick, J. L. (2023). Advice for improving the reproducibility of data extraction in meta‐analysis. Research Synthesis Methods, 14(6), 911–915. Portico. https://doi.org/10.1002/jrsm.1663", + "auto_ref": true + }, + { + "doi": "10.1038/s41562-019-0787-z", + "apa": "Kvarven, A., Strømland, E., & Johannesson, M. (2019). Comparing meta-analyses and preregistered multiple-laboratory replication projects. Nature Human Behaviour, 4(4), 423–434. https://doi.org/10.1038/s41562-019-0787-z", + "auto_ref": true + }, + { + "doi": "10.1136/bmj.333.7568.597", + "apa": "Lau, J., Ioannidis, J. P. A., Terrin, N., Schmid, C. H., & Olkin, I. (2006). The case of the misleading funnel plot. 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J., ter Schure, J., Tentori, K., van Ravenzwaaij, D., Vandekerckhove, J., & Gundersen, O. E. (2025). How can we make sound replication decisions? Proceedings of the National Academy of Sciences, 122(5). https://doi.org/10.1073/pnas.2401236121", + "auto_ref": true + }, + { + "doi": "", + "apa": "Devezer, B., & Buzbas, E. O. (2025). Minimum viable experiment to replicate. PhilSci Archive. https://philsci-archive.pitt.edu/24738/", + "auto_ref": false + }, + { + "doi": "10.1098/rsos.242057", + "apa": "Dudda, L., Kormann, E., Kozula, M., DeVito, N. J., Klebel, T., Dewi, A. P. M., Spijker, R., Stegeman, I., Van den Eynden, V., Ross-Hellauer, T., & Leeflang, M. M. G. (2025). Open science interventions to improve reproducibility and replicability of research: a scoping review. Royal Society Open Science, 12(4). https://doi.org/10.1098/rsos.242057", + "auto_ref": true + }, + { + "doi": "10.1007/s42113-024-00220-w", + "apa": "Field, S. M., Volz, L., Kaznatcheev, A., & van Dongen, N. (2024). Can a Good Theory Be Built Using Bad Ingredients? Computational Brain & Behavior, 7(4), 608–615. https://doi.org/10.1007/s42113-024-00220-w", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-016-9858-y", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2016). Promoting Virtue or Punishing Fraud: Mapping Contrasts in the Language of ‘Scientific Integrity.’ Science and Engineering Ethics, 23(6), 1461–1485. https://doi.org/10.1007/s11948-016-9858-y", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0186281", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2017). The ghosts of HeLa: How cell line misidentification contaminates the scientific literature. PLOS ONE, 12(10), e0186281. https://doi.org/10.1371/journal.pone.0186281", + "auto_ref": true + }, + { + "doi": "10.1186/s41073-018-0051-5", + "apa": "Horbach, S. P. J. M., & Halffman, W. ( W. (2018). The changing forms and expectations of peer review. Research Integrity and Peer Review, 3(1). https://doi.org/10.1186/s41073-018-0051-5", + "auto_ref": true + }, + { + "doi": "10.1007/s11192-018-2969-2", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2018). The ability of different peer review procedures to flag problematic publications. Scientometrics, 118(1), 339–373. https://doi.org/10.1007/s11192-018-2969-2", + "auto_ref": true + }, + { + "doi": "10.1016/j.respol.2017.09.004", + "apa": "Horbach, S. P. J. M. (Serge), & Halffman, W. (Willem). (2019). The extent and causes of academic text recycling or ‘self-plagiarism.’ Research Policy, 48(2), 492–502. https://doi.org/10.1016/j.respol.2017.09.004", + "auto_ref": true + }, + { + "doi": "10.1007/s11024-019-09388-z", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2019). Journal Peer Review and Editorial Evaluation: Cautious Innovator or Sleepy Giant? Minerva, 58(2), 139–161. https://doi.org/10.1007/s11024-019-09388-z", + "auto_ref": true + }, + { + "doi": "10.1093/reseval/rvaa037", + "apa": "Horbach, S. P. J. M. (2021). No time for that now! Qualitative changes in manuscript peer review during the Covid-19 pandemic. Research Evaluation, 30(3), 231–239. https://doi.org/10.1093/reseval/rvaa037", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pmed.0020124", + "apa": "Ioannidis, J. P. A. (2005). Why Most Published Research Findings Are False. PLoS Medicine, 2(8), e124. https://doi.org/10.1371/journal.pmed.0020124", + "auto_ref": true + }, + { + "doi": "10.1177/25152459241296397", + "apa": "Lengersdorff, L. L., & Lamm, C. (2025). With Low Power Comes Low Credibility? Toward a Principled Critique of Results From Underpowered Tests. Advances in Methods and Practices in Psychological Science, 8(1). https://doi.org/10.1177/25152459241296397", + "auto_ref": true + }, + { + "doi": "10.1177/25152459231202724", + "apa": "Pownall, M., Pennington, C. R., Norris, E., Juanchich, M., Smailes, D., Russell, S., Gooch, D., Evans, T. R., Persson, S., Mak, M. H. C., Tzavella, L., Monk, R., Gough, T., Benwell, C. S. Y., Elsherif, M., Farran, E., Gallagher-Mitchell, T., Kendrick, L. T., Bahnmueller, J., … Clark, K. (2023). Evaluating the Pedagogical Effectiveness of Study Preregistration in the Undergraduate Dissertation. Advances in Methods and Practices in Psychological Science, 6(4). https://doi.org/10.1177/25152459231202724", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/4tpk8_v2", + "apa": "Rubin, M. (2025). What is critical metascience and why is it important? https://doi.org/10.31234/osf.io/4tpk8_v2", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0281086", + "apa": "Spitzer, L., & Mueller, S. (2023). Registered report: Survey on attitudes and experiences regarding preregistration in psychological research. PLOS ONE, 18(3), e0281086. https://doi.org/10.1371/journal.pone.0281086", + "auto_ref": true + }, + { + "doi": "", + "apa": "Syed, M. (2023). Some Data Indicating that Editors and Reviewers Do Not Check Preregistrations during the Review Process. https://osf.io/nh7qw/", + "auto_ref": false + }, + { + "doi": "10.31235/osf.io/pqc4v_v1", + "apa": "Ulpts, S., Bartscherer, S. F., Field, S. M., & Penders, B. (2025). The social replication of replication: Moving replication through epistemic communities. https://doi.org/10.31235/osf.io/pqc4v_v1", + "auto_ref": true + }, + { + "doi": "10.3758/s13428-023-02277-0", + "apa": "van den Akker, O. R., van Assen, M. A. L. M., Bakker, M., Elsherif, M., Wong, T. K., & Wicherts, J. M. (2023). Preregistration in practice: A comparison of preregistered and non-preregistered studies in psychology. Behavior Research Methods, 56(6), 5424–5433. https://doi.org/10.3758/s13428-023-02277-0", + "auto_ref": true + } + ] + }, + { + "name": "Purposes of replication attempts - what is a ‘failed’ replication?", + "description": "Explains the diverse aims of replication and clarifies that “failure” is not a verdict on truth but evidence about effect size, robustness, and conditions. Encourages nuanced interpretation (e.g., meta-analytic and design-aware) over binary success/failure narratives and highlights responsible communication of discrepant findings.", + "publications": [ + { + "doi": "", + "apa": "Fidler, F., & Wilcox, J. (2021). Reproducibility of scientific results. In E. N. Zalta (Ed.), The Stanford encyclopedia of philosophy. https://plato.stanford.edu/archives/sum2021/entries/scientific-reproducibility", + "auto_ref": false + }, + { + "doi": "10.1177/1745691612460686", + "apa": "Frank, M. C., & Saxe, R. (2012). Teaching Replication. Perspectives on Psychological Science, 7(6), 600–604. https://doi.org/10.1177/1745691612460686", + "auto_ref": true + }, + { + "doi": "10.1093/isp/ekv011", + "apa": "Martel García, F. (2016). Replication and the Manufacture of Scientific Inferences: A Formal Approach. International Studies Perspectives, ekv011. https://doi.org/10.1093/isp/ekv011", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pbio.3000691", + "apa": "Nosek, B. A., & Errington, T. M. (2020). What is replication? PLOS Biology, 18(3), e3000691. https://doi.org/10.1371/journal.pbio.3000691", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/hmnrx", + "apa": "Schimmelpfennig, R., Spicer, R., White, C., Gervais, W. M., Norenzayan, A., Heine, S., Henrich, J., & Muthukrishna, M. (2023). A Problem in Theory and More: Measuring the Moderating Role of Culture in Many Labs 2. https://doi.org/10.31234/osf.io/hmnrx", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.1521897113", + "apa": "Van Bavel, J. J., Mende-Siedlecki, P., Brady, W. J., & Reinero, D. A. (2016). Contextual sensitivity in scientific reproducibility. Proceedings of the National Academy of Sciences, 113(23), 6454–6459. https://doi.org/10.1073/pnas.1521897113", + "auto_ref": true + }, + { + "doi": "10.1017/S0140525X17001972", + "apa": "Zwaan, R. A., Etz, A., Lucas, R. E., & Donnellan, M. B. (2017). Making replication mainstream. Behavioral and Brain Sciences, 41. https://doi.org/10.1017/s0140525x17001972", + "auto_ref": true + } + ] + }, + { + "name": "Registered Replication Reports", + "description": "Registered Reports are studies that are peer-reviewed prior to data collection, with an agreement between the journal and the author(s) that it will be published regardless of outcome as long as the preregistered methods are reasonably followed. Registered REPLICATION Reports are a special category of these that only include replications.", + "publications": [ + { + "doi": "10.1177/1745691614545653", + "apa": "Alogna, V. K., Attaya, M. K., Aucoin, P., Bahník, Š., Birch, S., Birt, A. R., Bornstein, B. H., Bouwmeester, S., Brandimonte, M. A., Brown, C., Buswell, K., Carlson, C., Carlson, M., Chu, S., Cislak, A., Colarusso, M., Colloff, M. F., Dellapaolera, K. S., Delvenne, J.-F., … Zwaan, R. A. (2014). Registered Replication Report. Perspectives on Psychological Science, 9(5), 556–578. https://doi.org/10.1177/1745691614545653", + "auto_ref": true + }, + { + "doi": "", + "apa": "Anon. (n.d.). Ongoing Replication Projects. Association for Psychological Science - APS. https://www.psychologicalscience.org/publications/replication/ongoing-projects", + "auto_ref": false + }, + { + "doi": "10.1038/s41562-021-01193-7", + "apa": "Chambers, C. D., & Tzavella, L. (2021). The past, present and future of Registered Reports. Nature Human Behaviour, 6(1), 29–42. https://doi.org/10.1038/s41562-021-01193-7", + "auto_ref": true + }, + { + "doi": "10.1177/1745691615605826", + "apa": "Eerland, A., Sherrill, A. M., Magliano, J. P., Zwaan, R. A., Arnal, J. D., Aucoin, P., Berger, S. A., Birt, A. R., Capezza, N., Carlucci, M., Crocker, C., Ferretti, T. R., Kibbe, M. R., Knepp, M. M., Kurby, C. A., Melcher, J. M., Michael, S. W., Poirier, C., & Prenoveau, J. M. (2016). Registered Replication Report. Perspectives on Psychological Science, 11(1), 158–171. https://doi.org/10.1177/1745691615605826", + "auto_ref": true + }, + { + "doi": "10.1177/1745691614543974", + "apa": "Simons, D. J., Holcombe, A. O., & Spellman, B. A. (2014). An Introduction to Registered Replication Reports at Perspectives on Psychological Science. Perspectives on Psychological Science, 9(5), 552–555. https://doi.org/10.1177/1745691614543974", + "auto_ref": true + } + ] + }, + { + "name": "The politics of replicating famous studies", + "description": "Sometimes responses to replication research can be negative. Failed replications of famous work, most notably power posing, ego depletion, stereotype threat, and facial feedback[ah][ai], have received a lot of attention.", + "publications": [ + { + "doi": "10.1371/journal.pone.0029081", + "apa": "Doyen, S., Klein, O., Pichon, C.-L., & Cleeremans, A. (2012). Behavioral Priming: It’s All in the Mind, but Whose Mind? PLoS ONE, 7(1), e29081. https://doi.org/10.1371/journal.pone.0029081", + "auto_ref": true + }, + { + "doi": "", + "apa": "Neuliep, J. W., & Crandall, R. (1990). Editorial bias against replication research. Journal of Social Behavior & Personality, 5(4), 85-90.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Neuliep, J. W., & Crandall, R. (1993). Reviewer bias against replication research. Journal of Social Behavior & Personality, 8(6), 21-29.", + "auto_ref": false + } + ] + } + ] + }, + { + "number": 9, + "name": "Academic Structures and Institutions", + "description": "Attainment of a grounding in topics related to academia and academics. Students should understand how individuals, teams, institutions, and academic culture work together to promote (or hinder) openness, inclusion, diversity, equity, and transparency. Gathering perspectives on navigating scientific and academic life. Learning the challenges and rewards in the academic setting, the “hidden curriculum” in academic life. There are 17 sub-clusters which aim to further parse the learning and teaching process:", + "sub_clusters": [ + { + "name": "Accessibility", + "description": "Accessibility refers to making data, research environments, teaching and research outputs usable (e.g. Universal Design and hybrid participation options) by as many people as possible.", + "publications": [ + { + "doi": "10.1002/ece3.7009", + "apa": "Geange, S. R., von Oppen, J., Strydom, T., Boakye, M., Gauthier, T. J., Gya, R., Halbritter, A. H., Jessup, L. H., Middleton, S. L., Navarro, J., Pierfederici, M. E., Chacón‐Labella, J., Cotner, S., Farfan‐Rios, W., Maitner, B. S., Michaletz, S. T., Telford, R. J., Enquist, B. J., & Vandvik, V. (2020). Next‐generation field courses: Integrating Open Science and online learning. Ecology and Evolution, 11(8), 3577–3587. Portico. https://doi.org/10.1002/ece3.7009", + "auto_ref": true + }, + { + "doi": "10.3389/fpsyg.2023.1093290", + "apa": "Hamilton, L. G., & Petty, S. (2023). Compassionate pedagogy for neurodiversity in higher education: A conceptual analysis. Frontiers in Psychology, 14. https://doi.org/10.3389/fpsyg.2023.1093290", + "auto_ref": true + }, + { + "doi": "10.1016/j.compedu.2018.11.006", + "apa": "Nightingale, K. P., Anderson, V., Onens, S., Fazil, Q., & Davies, H. (2019). Developing the inclusive curriculum: Is supplementary lecture recording an effective approach in supporting students with Specific Learning Difficulties (SpLDs)? Computers & Education, 130, 13–25. https://doi.org/10.1016/j.compedu.2018.11.006", + "auto_ref": true + }, + { + "doi": "10.1007/s10734-020-00674-4", + "apa": "Nordmann, E., Clark, A., Spaeth, E., & MacKay, J. R. D. (2021). Lights, camera, active! appreciation of active learning predicts positive attitudes towards lecture capture. Higher Education, 83(3), 481–502. https://doi.org/10.1007/s10734-020-00674-4", + "auto_ref": true + }, + { + "doi": "", + "apa": "Nordmann, E., Hutchison, J., MacKay, J.R.D. (2021). Lecture rapture: the place and case for lectures in the new normal. Teaching in Higher Education, 27(5), 709-716. https:doi.org/10.1080/13562517.2021.2015755", + "auto_ref": false + }, + { + "doi": "10.13021/jipe.2020.2731", + "apa": "Prohn, S., Hall, T., Kunkes, I., McTague, B., & Russell, C. (2020). Leveraging Campus Collaboration to Promote Sustainable, Inclusive Writing Support for All Students. Journal of Inclusive Postsecondary Education, Vol. 2 No. 2 (2020): Journal of Inclusive Postsecondary Education. https://doi.org/10.13021/JIPE.2020.2731", + "auto_ref": true + }, + { + "doi": "10.1111/spc3.12847", + "apa": "Puthillam, A., Montilla Doble, L. J., Delos Santos, J. J. I., Elsherif, M. M., Steltenpohl, C. N., Moreau, D., Pownall, M., Silverstein, P., Anand‐Vembar, S., & Kapoor, H. (2023). Guidelines to improve internationalization in the psychological sciences. Social and Personality Psychology Compass, 18(1). Portico. https://doi.org/10.1111/spc3.12847", + "auto_ref": true + }, + { + "doi": "", + "apa": "Steinfeld, E., & Maisel, J. (2012). Universal design: Creating inclusive environments. John Wiley & Sons. https://content.e-bookshelf.de/media/reading/L-592705-5ce358b130.pdf", + "auto_ref": false + } + ] + }, + { + "name": "Citation Politics & Practices", + "description": "Citation is fundamental for academic writing to acknowledge the ideas and work of authors influenced and informed our own writing. However, the politics of citations perpetuates power imbalance especially for race, gender and neurodivergence. Under-represented individuals (e.g. ethnic minority individuals, women, LGBTQIA2S+ and neurodivergent individuals) tend to be ignored in scholarship, while a small group of white, heterosexual, neurotypical men dominate the scholar discourse and cite themselves. This section provides information detailing the under-represented groups that are under-cited and how a citation diversity statement can be a solution to reduce inequality in citation politics.", + "publications": [ + { + "doi": "10.36850/mr8", + "apa": "Bennett, A., Garside, D., Gould van Praag, C., Hostler, T. J., Kherroubi Garcia, I., Plomp, E., Schettino, A., Teplitzky, S., & Ye, H. (2023). A Manifesto for Rewarding and Recognizing Team Infrastructure Roles. Journal of Trial and Error, 4(1), 60–72. KB. https://doi.org/10.36850/mr8", + "auto_ref": true + }, + { + "doi": "10.1162/qss_c_00274", + "apa": "Devezer, B., & Penders, B. (2023). Scientific reform, citation politics and the bureaucracy of oblivion. Quantitative Science Studies, 4(4), 857–859. https://doi.org/10.1162/qss_c_00274", + "auto_ref": true + }, + { + "doi": "10.3389/fevo.2022.889236", + "apa": "Gould, J., & Valdez, J. W. (2022). The Gollum Effect: The Issue of Research Opportunity Guarding in Academia. Frontiers in Ecology and Evolution, 10. https://doi.org/10.3389/fevo.2022.889236", + "auto_ref": true + }, + { + "doi": "10.31222/osf.io/aqyhg", + "apa": "Horbach, S. P. J. M., Aagaard, K., & Schneider, J. W. (2021). Meta-Research: How problematic citing practices distort science. https://doi.org/10.31222/osf.io/aqyhg", + "auto_ref": true + }, + { + "doi": "10.1093/reseval/rvac016", + "apa": "Horbach, S. P. J. M., Oude Maatman, F. J. W., Halffman, W., & Hepkema, W. M. (2022). Automated citation recommendation tools encourage questionable citations. Research Evaluation, 31(3), 321–325. https://doi.org/10.1093/reseval/rvac016", + "auto_ref": true + }, + { + "doi": "10.1177/2378023117738903", + "apa": "King, M. M., Bergstrom, C. T., Correll, S. J., Jacquet, J., & West, J. D. (2017). Men Set Their Own Cites High: Gender and Self-citation across Fields and over Time. Socius: Sociological Research for a Dynamic World, 3. https://doi.org/10.1177/2378023117738903", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/6kvqg", + "apa": "Lawson, K. M., Murphy, B., Azpeitia, J., LOMBARD, E., & Pope, T. (2022). Citing decisions in psychology: A roadblock to cumulative and inclusive science. https://doi.org/10.31234/osf.io/6kvqg", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.2217564120", + "apa": "Marks, R. A., Amézquita, E. J., Percival, S., Rougon-Cardoso, A., Chibici-Revneanu, C., Tebele, S. M., Farrant, J. M., Chitwood, D. H., & VanBuren, R. (2023). A critical analysis of plant science literature reveals ongoing inequities. Proceedings of the National Academy of Sciences, 120(10). https://doi.org/10.1073/pnas.2217564120", + "auto_ref": true + }, + { + "doi": "10.1080/14680777.2018.1447395", + "apa": "Bailey, M. (2018). On misogynoir: citation, erasure, and plagiarism. Feminist Media Studies, 18(4), 762–768. https://doi.org/10.1080/14680777.2018.1447395", + "auto_ref": true + }, + { + "doi": "", + "apa": "Opara, I. (2022). How to protect research ideas as a junior scientist. Nature. https://www.nature.com/articles/d41586-022-03750-0", + "auto_ref": false + }, + { + "doi": "10.1038/s41586-022-04966-w", + "apa": "Ross, M. B., Glennon, B. M., Murciano-Goroff, R., Berkes, E. G., Weinberg, B. A., & Lane, J. I. (2022). Women are credited less in science than men. Nature, 608(7921), 135–145. https://doi.org/10.1038/s41586-022-04966-w", + "auto_ref": true + }, + { + "doi": "", + "apa": "Smith, C. A. (2018). Cite Black women: A critical praxis. www.citeblackwomencollective.org/our-praxis.html", + "auto_ref": false + }, + { + "doi": "10.1002/fea2.12040", + "apa": "Smith, C. A., Williams, E. L., Wadud, I. A., & Pirtle, W. N. L. (2021). Cite Black Women: A Critical Praxis (A Statement). Feminist Anthropology, 2(1), 10–17. Portico. https://doi.org/10.1002/fea2.12040", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-022-00793-1", + "apa": "Kwon, D. (2022). The rise of citational justice: how scholars are making references fairer. Nature, 603(7902), 568–571. https://doi.org/10.1038/d41586-022-00793-1", + "auto_ref": true + }, + { + "doi": "10.1080/09687599.2017.1411251", + "apa": "Waterfield, B., Beagan, B. B., & Weinberg, M. (2017). Disabled academics: a case study in Canadian universities. Disability & Society, 33(3), 327–348. https://doi.org/10.1080/09687599.2017.1411251", + "auto_ref": true + }, + { + "doi": "10.1080/23808985.2021.1960180", + "apa": "Wang, X., Dworkin, J. D., Zhou, D., Stiso, J., Falk, E. B., Bassett, D. S., Zurn, P., & Lydon-Staley, D. M. (2021). Gendered citation practices in the field of communication. Annals of the International Communication Association, 45(2), 134–153. https://doi.org/10.1080/23808985.2021.1960180", + "auto_ref": true + }, + { + "doi": "10.1016/j.tics.2020.06.009", + "apa": "Zurn, P., Bassett, D. S., & Rust, N. C. (2020). The Citation Diversity Statement: A Practice of Transparency, A Way of Life. Trends in Cognitive Sciences, 24(9), 669–672. https://doi.org/10.1016/j.tics.2020.06.009", + "auto_ref": true + } + ] + }, + { + "name": "Decolonizing Research Practices", + "description": "", + "publications": [ + { + "doi": "10.5964/jspp.v3i1.564", + "apa": "Adams, G., Dobles, I., Gómez, L. H., Kurtiş, T., & Molina, L. E. (2015). Decolonizing Psychological Science: Introduction to the Special Thematic Section. Journal of Social and Political Psychology, 3(1), 213–238. https://doi.org/10.5964/jspp.v3i1.564", + "auto_ref": true + }, + { + "doi": "10.2307/j.ctv1qv3j7.6", + "apa": "Albornoz, D., Huang, M., Martin, I. M., Mateus, M., Touré, A. Y., & Chan, L. (2020). Framing power: Tracing key discourses in open science policies. In Contextualizing openness: Situating open science (pp. 9–34). University of Ottawa Press. https://doi.org/10.2307/j.ctv1qv3j7.6", + "auto_ref": false + }, + { + "doi": "", + "apa": "Ahmed, S. (2017). Living a feminist life. Duke University Press.", + "auto_ref": false + }, + { + "doi": "10.5334/dsj-2020-043", + "apa": "Carroll, S. R., Garba, I., Figueroa-Rodríguez, O. L., Holbrook, J., Lovett, R., Materechera, S., Parsons, M., Raseroka, K., Rodriguez-Lonebear, D., Rowe, R., Sara, R., Walker, J. D., Anderson, J., & Hudson, M. (2020). The CARE Principles for Indigenous Data Governance. Data Science Journal, 19. https://doi.org/10.5334/dsj-2020-043", + "auto_ref": true + }, + { + "doi": "", + "apa": "Chilisa, B. (2012). Indigenous research methodologies. Sage.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Coulthard, G. S. (2014). Red skin, white masks: Rejecting the colonial politics of recognition. University of Minnesota Press.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Denzin, N. K., Lincoln, Y. S., & Smith, L. T. (Eds.). (2008). Handbook of critical and indigenous methodologies. Sage.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Fricker, M. (2007). Epistemic injustice: Power and the ethics of knowing. Oxford University Press.", + "auto_ref": false + }, + { + "doi": "10.1177/026858098700200401", + "apa": "Fals-Borda, O. (1987). The Application of Participatory Action-Research in Latin America. International Sociology, 2(4), 329–347. https://doi.org/10.1177/026858098700200401", + "auto_ref": true + }, + { + "doi": "", + "apa": "Fanon, F. (1963). The wretched of the earth (C. Farrington, Trans.). Grove Press.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Freire, P. (2000). Pedagogy of the oppressed (30th anniversary ed.). Continuum. (Original work published 1970)", + "auto_ref": false + }, + { + "doi": "", + "apa": "Quijano, A. (2000). 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Routledge.", + "auto_ref": false + }, + { + "doi": "10.1080/13645579.2025.2569255", + "apa": "Moosavi, L. (2025). An introduction to decolonial research. International Journal of Social Research Methodology, 28(6), 635–649. https://doi.org/10.1080/13645579.2025.2569255", + "auto_ref": true + }, + { + "doi": "", + "apa": "Smith, L. T. (2012). Decolonizing methodologies: Research and Indigenous peoples (2nd ed.). Zed Books.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Spivak, G. C. (1988). Can the subaltern speak? In C. Nelson & L. Grossberg (Eds.), Marxism and the interpretation of culture (pp. 271–313). University of Illinois Press.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Patel, L. (2015). Decolonizing educational research: From ownership to answerability. Routledge.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Simpson, L. B. (2017). 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Leveraging a collaborative consortium model of mentee/mentor training to foster career progression of underrepresented postdoctoral researchers and promote institutional diversity and inclusion. PLOS ONE, 15(9), e0238518. https://doi.org/10.1371/journal.pone.0238518", + "auto_ref": true + }, + { + "doi": "10.1038/s41562-020-0926-6", + "apa": "Roberson, M. L. (2020). On supporting early-career Black scholars. Nature Human Behaviour, 4(8), 773–773. https://doi.org/10.1038/s41562-020-0926-6", + "auto_ref": true + }, + { + "doi": "10.1177/0146167220947326", + "apa": "Skitka, L. J., Melton, Z. J., Mueller, A. B., & Wei, K. Y. (2020). The Gender Gap: Who Is (and Is Not) Included on Graduate-Level Syllabi in Social/Personality Psychology. Personality and Social Psychology Bulletin, 47(6), 863–872. https://doi.org/10.1177/0146167220947326", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pcbi.1010954", + "apa": "Zivony, A., Kardosh, R., Timmins, L., & Reggev, N. (2023). 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Bitch: A Revolutionary Guide to Sex, Evolution and the Female Animal. Doubleday UK.", + "auto_ref": false + }, + { + "doi": "10.31219/osf.io/ga5fb_v1", + "apa": "Field, S. M., & Pownall, M. (2025). Subjectivity is a Feature, not a Flaw: A Call to Unsilence the Human Element in Science. https://doi.org/10.31219/osf.io/ga5fb_v1", + "auto_ref": true + }, + { + "doi": "", + "apa": "Harding, S. (2015). Objectivity and Diversity.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Melanie, F. (2023, April 17). The Myth of Objective Data. The MIT Press Reader. https://thereader.mitpress.mit.edu/the-myth-of-objective-data/?s=03", + "auto_ref": false + } + ] + }, + { + "name": "Racism in science", + "description": "Addresses the legacy and continuing impact of racism in research contexts, from biased study designs to the underrepresentation and marginalization of researchers of color today. Encourages critical examination of how racial biases can affect who does science, what topics are studied, and how results are interpreted.", + "publications": [ + { + "doi": "10.1037/xge0001461", + "apa": "Aly, M., Colunga, E., Crockett, M. J., Goldrick, M., Gomez, P., Kung, F. Y. H., McKee, P. C., Pérez, M., Stilwell, S. M., & Diekman, A. B. (2023). Changing the culture of peer review for a more inclusive and equitable psychological science. Journal of Experimental Psychology: General, 152(12), 3546–3565. https://doi.org/10.1037/xge0001461", + "auto_ref": true + }, + { + "doi": "10.1111/hypa.12354", + "apa": "Bailey, A. (2017). Tracking Privilege‐Preserving Epistemic Pushback in Feminist and Critical Race Philosophy Classes. Hypatia, 32(4), 876–892. https://doi.org/10.1111/hypa.12354", + "auto_ref": true + }, + { + "doi": "10.1037/amp0000905", + "apa": "Buchanan, N. T., Perez, M., Prinstein, M. J., & Thurston, I. B. (2021). 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Data sharing in qualitative research: opportunities and concerns. MedEdPublish, 7, 255. https://doi.org/10.15694/mep.2018.0000255.1", + "auto_ref": true + }, + { + "doi": "10.1002/eahr.500044", + "apa": "Mozersky, J., Parsons, M., Walsh, H., Baldwin, K., McIntosh, T., & DuBois, J. M. (2020). Research Participant Views regarding Qualitative Data Sharing. Ethics & Human Research, 42(2), 13–27. Portico. https://doi.org/10.1002/eahr.500044", + "auto_ref": true + }, + { + "doi": "10.4067/S0718-090X2016000300785", + "apa": "Piñeiro, R., & Rosenblatt, F. (2016). Pre-analysis plans for qualitative research. Revista de Ciencia Política, 36(3), 785–796. https://doi.org/10.4067/S0718-090X2016000300785", + "auto_ref": false + }, + { + "doi": "10.31234/osf.io/5yw4z", + "apa": "Prosser, A. M. B., Hamshaw, R., Meyer, J., Bagnall, R., Blackwood, L., Huysamen, M., Jordan, A., Vasileiou, K., & Walter, Z. (2021). When open data closes the door: A critical examination of the past, present and the potential future for open data guidelines in journals. https://doi.org/10.31234/osf.io/5yw4z", + "auto_ref": true + }, + { + "doi": "", + "apa": "Qualitative Data Repository (n.d.). Guidance and resources. Qualitative Data Repository. https://qdr.syr.edu/guidance", + "auto_ref": false + }, + { + "doi": "", + "apa": "Roulston, K. (2019, May 9). Archiving qualitative data [Blog post]. QualPage: Examining the world through qualitative inquiry. https://qualpage.com/2019/05/09/archiving-qualitative-data", + "auto_ref": false + }, + { + "doi": "", + "apa": "Tamminen, K. A., Bohaker, H., Bundon, A., Gastaldo, D., Gladstone, B. M., Krmpotich, C., McDonough, M., & Smith, B. (2020). Building and supporting the use of digital research infrastructure among qualitative researchers. International Society of Qualitative Research in Sport and Exercise. https://alliancecan.ca/sites/default/files/2022-03/tamminen-et-al-ndrio-white-paper-qualitative-research.pdf", + "auto_ref": false + }, + { + "doi": "10.1016/j.socscimed.2016.08.004", + "apa": "Tsai, A. C., Kohrt, B. A., Matthews, L. T., Betancourt, T. S., Lee, J. K., Papachristos, A. V., Weiser, S. D., & Dworkin, S. L. (2016). Promises and pitfalls of data sharing in qualitative research. Social Science & Medicine, 169, 191–198. https://doi.org/10.1016/j.socscimed.2016.08.004", + "auto_ref": true + }, + { + "doi": "10.1177/10497323211054058", + "apa": "VandeVusse, A., Mueller, J., & Karcher, S. (2021). Qualitative Data Sharing: Participant Understanding, Motivation, and Consent. Qualitative Health Research, 32(1), 182–191. https://doi.org/10.1177/10497323211054058", + "auto_ref": true + }, + { + "doi": "10.5281/zenodo.8160880", + "apa": "Verburg, M., Braukmann, R., & Mahabier, W. (2023). 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Community of Practice for Naturally Occurring Data. https://osf.io/tv8g6", + "auto_ref": false + }, + { + "doi": "", + "apa": "Bosch, S., (2025). Supporting qualitative open science through institutional policy and infrastructure [Plenary slides]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/ezutr", + "auto_ref": false + }, + { + "doi": "", + "apa": "Bosch, S., (2025). Supporting qualitative open science through institutional policy and infrastructure [Video]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/ajdfb", + "auto_ref": false + }, + { + "doi": "", + "apa": "Branney, P. (2025). Open science and qualitative research: FAIR archiving, safeguarding, and stewarding of potentially identifiable qualitative data [Workshop]. Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/qv8f6", + "auto_ref": false + }, + { + "doi": "10.31222/osf.io/n5zkw", + "apa": "Cole, N. L., Ulpts, S., Bochynska, A., Kormann, E., Good, M., Leitner, B., & Ross-Hellauer, T. (2024). Reproducibility and replicability of qualitative research: an integrative review of concepts, barriers and enablers. https://doi.org/10.31222/osf.io/n5zkw", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0125208", + "apa": "Cummings, J. A., Zagrodney, J. M., & Day, T. E. (2015). Impact of Open Data Policies on Consent to Participate in Human Subjects Research: Discrepancies between Participant Action and Reported Concerns. PLOS ONE, 10(5), e0125208. https://doi.org/10.1371/journal.pone.0125208", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/6z9c3_v1", + "apa": "Field, S. M. (2025). Open With Care! 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Perspectives on Politics, 19(1), 171–208. https://doi.org/10.1017/s1537592720001164", + "auto_ref": true + }, + { + "doi": "10.17863/CAM.62157", + "apa": "Jarman, B. (2020). Open Data and sensitive interviews: Reflecting on ethics, consent, and reproducibility. Apollo - University of Cambridge Repository. https://doi.org/10.17863/CAM.62157", + "auto_ref": true + }, + { + "doi": "", + "apa": "Joyce, J. B., & Douglass, T. (2025). Practicalities of qualitative data sharing [Workshop]. Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/nrv9w", + "auto_ref": false + }, + { + "doi": "", + "apa": "Kapiszewski, D., Karcher S., SSRC & Qualitative Data Repository. (n.d.). Managing qualitative social science data [Online course]. Social Science Research Council. https://managing-qualitative-data.org", + "auto_ref": false + }, + { + "doi": "10.3389/fsoc.2024.1308029", + "apa": "Khan, S., Hirsch, J. S., & Zeltzer-Zubida, O. (2024). A dataset without a code book: ethnography and open science. Frontiers in Sociology, 9. https://doi.org/10.3389/fsoc.2024.1308029", + "auto_ref": true + }, + { + "doi": "", + "apa": "Korkiakangas, T. (2014). Challenges in archiving and sharing video data: Considering moral, pragmatic, and substantial arguments. Journal of Research Practice, 10(1), Article M3. https://discovery.ucl.ac.uk/id/eprint/10019201/1/Challenges_in_Video_Data_PRE_PRINT.pdf", + "auto_ref": false + }, + { + "doi": "10.1177/13591053241237620", + "apa": "Lamb, D., Russell, A., Morant, N., & Stevenson, F. (2024). The challenges of open data sharing for qualitative researchers. Journal of Health Psychology, 29(7), 659–664. https://doi.org/10.1177/13591053241237620", + "auto_ref": true + }, + { + "doi": "10.1177/0002764218784991", + "apa": "Mannheimer, S., Pienta, A., Kirilova, D., Elman, C., & Wutich, A. (2018). Qualitative Data Sharing: Data Repositories and Academic Libraries as Key Partners in Addressing Challenges. American Behavioral Scientist, 63(5), 643–664. https://doi.org/10.1177/0002764218784991", + "auto_ref": true + }, + { + "doi": "10.15694/mep.2018.0000255.1", + "apa": "McGrath, C., & Nilsonne, G. (2018). Data sharing in qualitative research: opportunities and concerns. MedEdPublish, 7, 255. https://doi.org/10.15694/mep.2018.0000255.1", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0261719", + "apa": "Mozersky, J., McIntosh, T., Walsh, H. A., Parsons, M. V., Goodman, M., & DuBois, J. M. (2021). Barriers and facilitators to qualitative data sharing in the United States: A survey of qualitative researchers. PLOS ONE, 16(12), e0261719. https://doi.org/10.1371/journal.pone.0261719", + "auto_ref": true + }, + { + "doi": "10.1002/eahr.500044", + "apa": "Mozersky, J., Parsons, M., Walsh, H., Baldwin, K., McIntosh, T., & DuBois, J. M. (2020). Research Participant Views regarding Qualitative Data Sharing. Ethics & Human Research, 42(2), 13–27. Portico. https://doi.org/10.1002/eahr.500044", + "auto_ref": true + }, + { + "doi": "10.1002/eahr.500044", + "apa": "Mozersky, J., Parsons, M., Walsh, H., Baldwin, K., McIntosh, T., & DuBois, J. M. (2020). Research Participant Views regarding Qualitative Data Sharing. Ethics & Human Research, 42(2), 13–27. Portico. https://doi.org/10.1002/eahr.500044", + "auto_ref": true + }, + { + "doi": "", + "apa": "Owoyele, B. A., Schilling, M., Sawahn, R., Kaemer, N., Zherebenkov, P., Verma, B., Pouw, W., & de Melo, G. (2025, March). Masking tactics and strategies for deidentifying audio-visual data in qualitative research [Workshop]. Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/apg9w", + "auto_ref": false + }, + { + "doi": "10.1177/13591053231225903", + "apa": "Prosser, A. M., Bagnall, R., & Higson-Sweeney, N. (2024). Reflection over compliance: Critiquing mandatory data sharing policies for qualitative research. Journal of Health Psychology, 29(7), 653–658. https://doi.org/10.1177/13591053231225903", + "auto_ref": true + }, + { + "doi": "10.1111/bjso.12576", + "apa": "Prosser, A. M. B., Hamshaw, R. J. T., Meyer, J., Bagnall, R., Blackwood, L., Huysamen, M., Jordan, A., Vasileiou, K., & Walter, Z. (2022). When open data closes the door: A critical examination of the past, present and the potential future for open data guidelines in journals. British Journal of Social Psychology, 62(4), 1635–1653. Portico. https://doi.org/10.1111/bjso.12576", + "auto_ref": true + }, + { + "doi": "10.5210/fm.v19i9.5381", + "apa": "Scheliga, K., & Friesike, S. (2014). Putting open science into practice: A social dilemma? First Monday. https://doi.org/10.5210/fm.v19i9.5381", + "auto_ref": true + }, + { + "doi": "", + "apa": "Tamminen, K. A., Bohaker, H., Bundon, A., Gastaldo, D., Gladstone, B. M., Krmpotich, C., McDonough, M., & Smith, B. (2020). Building and supporting the use of digital research infrastructure among qualitative researchers. International Society of Qualitative Research in Sport and Exercise. https://alliancecan.ca/sites/default/files/2022-03/tamminen-et-al-ndrio-white-paper-qualitative-research.pdf", + "auto_ref": false + }, + { + "doi": "10.1016/j.socscimed.2016.08.004", + "apa": "Tsai, A. C., Kohrt, B. A., Matthews, L. T., Betancourt, T. S., Lee, J. K., Papachristos, A. V., Weiser, S. D., & Dworkin, S. L. (2016). Promises and pitfalls of data sharing in qualitative research. Social Science & Medicine, 169, 191–198. https://doi.org/10.1016/j.socscimed.2016.08.004", + "auto_ref": true + }, + { + "doi": "", + "apa": "van Ravenzwaaij, D., de Jong, M., Hoekstra, R., Scheibe, S., Span, M. M., Wessel, I., & Heininga, V. E. (2025). De-Identification When Making Data Sets Findable, Accessible, Interoperable, and Reusable (FAIR): Two Worked Examples From the Behavioral and Social Sciences. Advances in Methods and Practices in Psychological Science, 8(2), 25152459251336130.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Whylly, K. E., Karcher, S., & Renbarger, R. (2023, January 25). Data sharing for qualitative research: Webinar and panel. Center for Open Science. https://youtu.be/eWZvmSIfhQY", + "auto_ref": false + }, + { + "doi": "", + "apa": "Yardley SJ, Watts KM, Pearson J, Richardson JC. Ethical Issues in the Reuse of Qualitative Data: Perspectives From Literature, Practice, and Participants. Qualitative Health Research. 2013;24(1):102-113. doi:10.1177/1049732313518373", + "auto_ref": false + } + ] + }, + { + "name": "Philosophical underpinnings of qualitative research", + "description": "Qualitative researchers tend to approach research from a non-positivist perspective, which affects the kinds of questions qualitative researchers ask, the methodology they use, and the types of conclusions they want to draw. Thus, qualitative researchers have their own way of interacting (or not) with open science practices. These resources will help readers understand how qualitative researchers approach research, and by extension, open science.", + "publications": [ + { + "doi": "", + "apa": "Braun, V. & Clarke, V. (2014). Successful qualitative research: A practical guide for beginners. Sage Publications.", + "auto_ref": false + }, + { + "doi": "10.1191/1478088706qp063oa", + "apa": "Braun, V., & Clarke, V. (2006). Using thematic analysis in psychology. Qualitative Research in Psychology, 3(2), 77–101. https://doi.org/10.1191/1478088706qp063oa", + "auto_ref": true + }, + { + "doi": "", + "apa": "Creswell, J. W., & Poth, C. N. (2017). Qualitative inquiry and research design: Choosing among five approaches. Sage Publications.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Mackenzie, N., & Knipe, S. (2006). Research dilemmas: Paradigms, methods and methodology. Issues in Educational Research, 16(2), 193–205. http://www.iier.org.au/iier16/mackenzie.html", + "auto_ref": false + }, + { + "doi": "10.1016/j.math.2012.03.006", + "apa": "Petty, N. J., Thomson, O. P., & Stew, G. (2012). Ready for a paradigm shift? Part 1: Introducing the philosophy of qualitative research. Manual Therapy, 17(4), 267–274. https://doi.org/10.1016/j.math.2012.03.006", + "auto_ref": true + }, + { + "doi": "10.1007/s43545-023-00774-9", + "apa": "Phillips, M. J. (2023). Towards a social constructionist, criticalist, Foucauldian-informed qualitative research approach: Opportunities and challenges. SN Social Sciences, 3(10). https://doi.org/10.1007/s43545-023-00774-9", + "auto_ref": true + }, + { + "doi": "", + "apa": "Pownall, M., Talbot, C. V., Henschel, A., Lautarescu, A., Lloyd, K. E., Hartmann, H., ... & Siegel, J. A. (2021). Navigating open science as early career feminist researchers. Psychology of Women Quarterly, 45(4), 526-539.", + "auto_ref": false + }, + { + "doi": "10.1093/oxfordhb/9780199811755.001.0001", + "apa": "Leavy, P. (Ed.). (2014). The Oxford Handbook of Qualitative Research. https://doi.org/10.1093/oxfordhb/9780199811755.001.0001", + "auto_ref": true + }, + { + "doi": "10.1017/S1537592720004703", + "apa": "Kapiszewski, D., & Wood, E. J. (2021). Ethics, Epistemology, and Openness in Research with Human Participants. Perspectives on Politics, 20(3), 948–964. https://doi.org/10.1017/s1537592720004703", + "auto_ref": true + }, + { + "doi": "", + "apa": "Prosser, A., (2025). Unheard, or unspoken? How listening to qualitative researcher voices will shape the future of open research [Video]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Plenary session). Community of Practice for Naturally Occurring Data. https://osf.io/pxcy5", + "auto_ref": false + }, + { + "doi": "", + "apa": "Prosser, A., (2025). Unheard, or unspoken? How listening to qualitative researcher voices will shape the future of open research [Plenary slides]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Plenary session). Community of Practice for Naturally Occurring Data. https://osf.io/vnm7p", + "auto_ref": false + }, + { + "doi": "", + "apa": "Cole, N. L., (2025). Why the Open Science movement needs qualitative researchers. [Video]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Plenary session). Community of Practice for Naturally Occurring Data. https://osf.io/sgbvj", + "auto_ref": false + }, + { + "doi": "", + "apa": "Cole, N. L., (2025). Why the Open Science movement needs qualitative researchers. [Plenary slides]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Plenary session). Community of Practice for Naturally Occurring Data. https://osf.io/sgrhk", + "auto_ref": false + }, + { + "doi": "10.31219/osf.io/ga5fb_v1", + "apa": "Field, S. M., & Pownall, M. (2025). Subjectivity is a Feature, not a Flaw: A Call to Unsilence the Human Element in Science. https://doi.org/10.31219/osf.io/ga5fb_v1", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/6z9c3_v1", + "apa": "Field, S. M. (2025). Open With Care! Consent, Context, and Co-production in Open Qualitative Research. https://doi.org/10.31219/osf.io/6z9c3_v1", + "auto_ref": true + } + ] + }, + { + "name": "Preregistration and Registered reports", + "description": "Preregistration and registered reports may be useful for qualitative researchers who are hoping to confirm hypotheses. Preregistration may also be a helpful tool for reflexivity for some qualitative researchers.", + "publications": [ + { + "doi": "", + "apa": "Hartman, A., Kern, F. G., & Mellor, D. T. (2018). Preregistration for Qualitative Research Template. Open Science Framework. https://osf.io/j7ghv/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Haven, T., Rosenblatt, F., Pineiro, R., & Kern, F. G. (2020). Qualitative preregistration. [Blog] Center for Open Science. https://www.cos.io/blog/qualitative-preregistration", + "auto_ref": false + }, + { + "doi": "10.1080/08989621.2019.1580147", + "apa": "L. Haven, T., & Van Grootel, Dr. L. (2019). Preregistering qualitative research. Accountability in Research, 26(3), 229–244. https://doi.org/10.1080/08989621.2019.1580147", + "auto_ref": true + }, + { + "doi": "10.1177/1609406920976417", + "apa": "Haven, T. L., Errington, T. M., Gleditsch, K. S., van Grootel, L., Jacobs, A. M., Kern, F. G., Piñeiro, R., Rosenblatt, F., & Mokkink, L. B. (2020). Preregistering Qualitative Research: A Delphi Study. International Journal of Qualitative Methods, 19. https://doi.org/10.1177/1609406920976417", + "auto_ref": true + }, + { + "doi": "", + "apa": "Haven, T. L. (2020). OSCG workshop “Preregistration of Qualitative Research” [Video]. YouTube. https://www.youtube.com/watch?v=BNf9totTA_4", + "auto_ref": false + }, + { + "doi": "", + "apa": "Center for Open Science. (n.d.). Registered Reports: Peer review before results are known to align scientific values and practices. https://www.cos.io/initiatives/registered-reports", + "auto_ref": false + }, + { + "doi": "10.1038/s41562-021-01265-8", + "apa": "Karhulahti, V.-M. (2022). Registered reports for qualitative research. Nature Human Behaviour, 6(1), 4–5. https://doi.org/10.1038/s41562-021-01265-8", + "auto_ref": true + }, + { + "doi": "", + "apa": "Kern, Florian & Gleditsch, Kristian. (2017). Exploring Pre-registration and Pre-analysis Plans for Qualitative Inference. 10.13140/RG.2.2.14428.69769.", + "auto_ref": false + }, + { + "doi": "", + "apa": "Silverstein, P., Pennington, C., Branney, P., O’Connor, D., Lawlor, E., O’Brien, E., & Lynott, D. (2024). A registered report survey of open research practices in psychology departments in the UK and Ireland. British Journal of Psychology, 115: 497-534", + "auto_ref": false + }, + { + "doi": "", + "apa": "https://bpspsychub.onlinelibrary.wiley.com/doi/pdf/10.1111/ bjop.12700", + "auto_ref": false + }, + { + "doi": "10.36850/mr7", + "apa": "Steltenpohl, C. N., Lustick, H., Meyer, M. S., Lee, L. E., Stegenga, S. M., Standiford Reyes, L., & Renbarger, R. L. (2023). Rethinking Transparency and Rigor from a Qualitative Open Science Perspective. Journal of Trial and Error, 4(1), 47–59. KB. https://doi.org/10.36850/mr7", + "auto_ref": true + } + ] + }, + { + "name": "Qualitative approaches to open science", + "description": "This section contains articles that outline what open science can look like from a qualitative approach. These articles also outline several places where there may be tensions between mainstream, quantitatively-focused open science perspectives and those often held by qualitative researchers.", + "publications": [ + { + "doi": "10.1177/03616843211036460", + "apa": "Bennett, E. A. (2021). Open Science From a Qualitative, Feminist Perspective: Epistemological Dogmas and a Call for Critical Examination. Psychology of Women Quarterly, 45(4), 448–456. https://doi.org/10.1177/03616843211036460", + "auto_ref": true + }, + { + "doi": "", + "apa": "Bochynska, A., et al. (2025). Supporting the adoption of open science practices by qualitative researchers [Plenary slides]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/xdw3m", + "auto_ref": false + }, + { + "doi": "", + "apa": "Bochynska, A., et al. (2025). Supporting the adoption of open science practices by qualitative researchers [Video]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/tv8g6", + "auto_ref": false + }, + { + "doi": "", + "apa": "Bosch, S., (2025). Supporting qualitative open science through institutional policy and infrastructure [Video]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/ajdfb", + "auto_ref": false + }, + { + "doi": "", + "apa": "Bosch, S., (2025) Supporting qualitative open science through institutional policy and infrastructure [Plenary slides]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/ezutr", + "auto_ref": false + }, + { + "doi": "10.1177/16094069211034641", + "apa": "Class, B., de Bruyne, M., Wuillemin, C., Donzé, D., & Claivaz, J.-B. (2021). Towards Open Science for the Qualitative Researcher: From a Positivist to an Open Interpretation. International Journal of Qualitative Methods, 20. https://doi.org/10.1177/16094069211034641", + "auto_ref": true + }, + { + "doi": "10.1177/2158244016678912", + "apa": "Corti, L., & Fielding, N. (2016). Opportunities From the Digital Revolution. Sage Open, 6(4). https://doi.org/10.1177/2158244016678912", + "auto_ref": true + }, + { + "doi": "10.1093/joc/jqz052", + "apa": "Dienlin, T., Johannes, N., Bowman, N. D., Masur, P. K., Engesser, S., Kümpel, A. S., Lukito, J., Bier, L. M., Zhang, R., Johnson, B. K., Huskey, R., Schneider, F. M., Breuer, J., Parry, D. A., Vermeulen, I., Fisher, J. T., Banks, J., Weber, R., Ellis, D. A., … de Vreese, C. (2020). An Agenda for Open Science in Communication. Journal of Communication, 71(1), 1–26. https://doi.org/10.1093/joc/jqz052", + "auto_ref": true + }, + { + "doi": "10.5281/zenodo.2673016", + "apa": "Duckles, B. M., & Steeves, V. (2019). Qualitative Research Using Open Tools. https://doi.org/10.5281/ZENODO.2673016", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/e3cq4", + "apa": "Field, S. M., van Ravenzwaaij, D., Pittelkow, M.-M., Hoek, J. M., & Derksen, M. (2021). Qualitative Open Science – Pain Points and Perspectives. https://doi.org/10.31219/osf.io/e3cq4", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/6z9c3_v1", + "apa": "Field, S. M. (2025). Open With Care! Consent, Context, and Co-production in Open Qualitative Research. https://doi.org/10.31219/osf.io/6z9c3_v1", + "auto_ref": true + }, + { + "doi": "", + "apa": "García-Álvarez, E., & López Sintas, J. (2012). Open science, e-science and the new technologies: Challenges and old problems in qualitative research in the social sciences. Intangible Capital, 8(3), 497-519. http://hdl.handle.net/2099/12934", + "auto_ref": false + }, + { + "doi": "10.1108/AJIM-11-2019-0320", + "apa": "Hocker, J., Schindler, C., & Rittberger, M. (2020). Participatory design for ontologies: a case study of an open science ontology for qualitative coding schemas. Aslib Journal of Information Management, 72(4), 671–685. https://doi.org/10.1108/ajim-11-2019-0320", + "auto_ref": true + }, + { + "doi": "", + "apa": "Huang, R. (2016). RQDA: R-based qualitative data analysis (Version 0.2-8) [Computer software]. R Project. http://rqda.r-forge.r-project.org/", + "auto_ref": false + }, + { + "doi": "", + "apa": "Humphreys, L., Lewis Jr, N. A., Sender, K., & Won, A. S. (2021). Integrating qualitative methods and open science: Five principles for more trustworthy research. Journal of Communication, 71(5), 855-874.", + "auto_ref": false + }, + { + "doi": "10.1017/psa.2022.45", + "apa": "Leonelli, S. (2022). Open Science and Epistemic Diversity: Friends or Foes? Philosophy of Science, 89(5), 991–1001. https://doi.org/10.1017/psa.2022.45", + "auto_ref": true + }, + { + "doi": "10.1017/9781009416368", + "apa": "Leonelli, S. (2023). Philosophy of Open Science. https://doi.org/10.1017/9781009416368", + "auto_ref": true + }, + { + "doi": "10.1007/s10508-020-01851-3", + "apa": "Lorenz, T. K., & Holland, K. J. (2020). Response to Sakaluk (2020): Let’s Get Serious About Including Qualitative Researchers in the Open Science Conversation. Archives of Sexual Behavior, 49(8), 2761–2763. https://doi.org/10.1007/s10508-020-01851-3", + "auto_ref": true + }, + { + "doi": "10.1038/s44159-025-00477-3", + "apa": "Pownall, M. (2025). Bridging qualitative methods and open research. Nature Reviews Psychology, 4(9), 556–557. https://doi.org/10.1038/s44159-025-00477-3", + "auto_ref": true + }, + { + "doi": "", + "apa": "Pownall, M. (2025). Incorporating open science into qualitative methods teaching [Workshop]. Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/rfyju", + "auto_ref": false + }, + { + "doi": "10.1177/0001839219887663", + "apa": "Pratt, M. G., Kaplan, S., & Whittington, R. (2019). Editorial Essay: The Tumult over Transparency: Decoupling Transparency from Replication in Establishing Trustworthy Qualitative Research. Administrative Science Quarterly, 65(1), 1–19. https://doi.org/10.1177/0001839219887663", + "auto_ref": true + }, + { + "doi": "10.1525/collabra.284", + "apa": "Reischer, H. N., & Cowan, H. R. (2020). Quantity Over Quality? Reproducible Psychological Science from a Mixed Methods Perspective. Collabra: Psychology, 6(1). https://doi.org/10.1525/collabra.284", + "auto_ref": true + }, + { + "doi": "10.3233/EFI-190261", + "apa": "Schindler, C., Veja, C., Hocker, J., Kminek, H., & Meier, M. (2020). Collaborative open analysis in a qualitative research environment. Education for Information, 36(3), 247–261. https://doi.org/10.3233/efi-190261", + "auto_ref": true + }, + { + "doi": "10.1080/1750984X.2017.1317357", + "apa": "Smith, B., & McGannon, K. R. (2017). Developing rigor in qualitative research: problems and opportunities within sport and exercise psychology. International Review of Sport and Exercise Psychology, 11(1), 101–121. https://doi.org/10.1080/1750984x.2017.1317357", + "auto_ref": true + }, + { + "doi": "10.3233/EFI-190308", + "apa": "Steinhardt, I. (2020). Learning Open Science by doing Open Science. A reflection of a qualitative research project-based seminar. Education for Information, 36(3), 263–279. https://doi.org/10.3233/efi-190308", + "auto_ref": true + }, + { + "doi": "10.36850/mr7", + "apa": "Steltenpohl, C. N., Lustick, H., Meyer, M. S., Lee, L. E., Stegenga, S. M., Standiford Reyes, L., & Renbarger, R. L. (2023). Rethinking Transparency and Rigor from a Qualitative Open Science Perspective. Journal of Trial and Error, 4(1), 47–59. KB. https://doi.org/10.36850/mr7", + "auto_ref": true + }, + { + "doi": "10.1002/ev.20627", + "apa": "Steltenpohl, C. N., Standiford Reyes, L., Pei, M. A., & Lee, L. E. (2024). Open Science in Qualitative Evaluation: Considerations and Opportunities. New Directions for Evaluation, 2024(184), 35–40. Portico. https://doi.org/10.1002/ev.20627", + "auto_ref": true + }, + { + "doi": "", + "apa": "Tamminen, A. Bundon, B. Smith, M. H. McDonough, Z. A. Poucher & M. Atkinson (2021) Considerations for making informed choices about engaging in open qualitative research, Qualitative Research in Sport, Exercise and Health, 13:5, 864-886, DOI: 10.1080/2159676X.2021.1901138", + "auto_ref": false + }, + { + "doi": "10.1016/j.psychsport.2017.12.010", + "apa": "Tamminen, K. A., & Poucher, Z. A. (2018). Open science in sport and exercise psychology: Review of current approaches and considerations for qualitative inquiry. Psychology of Sport and Exercise, 36, 17–28. https://doi.org/10.1016/j.psychsport.2017.12.010", + "auto_ref": true + }, + { + "doi": "", + "apa": "van Burgsteden, L. (2025). Building qualitative open science communities: Challenges and opportunities [Workshop]. Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data https://osf.io/s7p9m", + "auto_ref": false + } + ] + }, + { + "name": "Reflexivity and positionality", + "description": "Reflexivity is an important practice within qualitative methods, and the critical examination of one’s position within a research study can lend itself to increased contextualization of and transparency in reporting.", + "publications": [ + { + "doi": "10.1007/s13194-020-00324-7", + "apa": "Field, S. M., & Derksen, M. (2020). Experimenter as automaton; experimenter as human: exploring the position of the researcher in scientific research. European Journal for Philosophy of Science, 11(1). https://doi.org/10.1007/s13194-020-00324-7", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/ga5fb_v1", + "apa": "Field, S. M., & Pownall, M. (2025). Subjectivity is a Feature, not a Flaw: A Call to Unsilence the Human Element in Science. https://doi.org/10.31219/osf.io/ga5fb_v1", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/6z9c3_v1", + "apa": "Field, S. M. (2025). Open With Care! Consent, Context, and Co-production in Open Qualitative Research. https://doi.org/10.31219/osf.io/6z9c3_v1", + "auto_ref": true + }, + { + "doi": "10.1080/02615470601118662", + "apa": "Fook, J., & Askeland, G. A. (2007). Challenges of Critical Reflection: ‘Nothing Ventured, Nothing Gained.’ Social Work Education, 26(5), 520–533. https://doi.org/10.1080/02615470601118662", + "auto_ref": true + }, + { + "doi": "10.1080/14623943.2015.1134471", + "apa": "Goldblatt, H., & Band-Winterstein, T. (2016). From understanding to insight: using reflexivity to promote students’ learning of qualitative research. Reflective Practice, 17(2), 100–113. https://doi.org/10.1080/14623943.2015.1134471", + "auto_ref": true + }, + { + "doi": "10.1177/1077800403262360", + "apa": "Guillemin, M., & Gillam, L. (2004). Ethics, Reflexivity, and “Ethically Important Moments” in Research. Qualitative Inquiry, 10(2), 261–280. https://doi.org/10.1177/1077800403262360", + "auto_ref": true + }, + { + "doi": "10.1285/i24212113v5i2p63", + "apa": "Hope, E. C., Brugh, C. S., & Nance, A. (2019). In search of a critical stance: Applying qualitative research practices for critical quantitative research in psychology (Version 1.0) [Data set]. University of Salento. https://doi.org/10.1285/I24212113V5I2P63", + "auto_ref": true + }, + { + "doi": "10.1111/spc3.12735", + "apa": "Jamieson, M. K., Govaart, G. H., & Pownall, M. (2023). Reflexivity in quantitative research: A rationale and beginner’s guide. Social and Personality Psychology Compass, 17(4). Portico. https://doi.org/10.1111/spc3.12735", + "auto_ref": true + }, + { + "doi": "10.1080/14780887.2017.1400144", + "apa": "Lazard, L., & McAvoy, J. (2017). Doing reflexivity in psychological research: What’s the point? What’s the practice? Qualitative Research in Psychology, 17(2), 159–177. https://doi.org/10.1080/14780887.2017.1400144", + "auto_ref": true + }, + { + "doi": "10.1177/1609406916681005", + "apa": "Mao, L., Mian Akram, A., Chovanec, D., & Underwood, M. L. (2016). Embracing the Spiral. International Journal of Qualitative Methods, 15(1). https://doi.org/10.1177/1609406916681005", + "auto_ref": true + }, + { + "doi": "", + "apa": "Pham, J., Perry-Wilson, T., Holmes, K., Schroeder, G., Reyes, A., & Pollok, M. (2025). The power of decolonizing research practices. The Professional Counselor, 15(1). https://tpcjournal.nbcc.org/the-power-of-decolonizing-research-practices", + "auto_ref": false + }, + { + "doi": "10.1002/ecs2.70168", + "apa": "Phurisamban, R., Luna, E., Eyster, H. N., Chignell, S., & Koppes, M. (2025). Shedding the cloak of neutrality: A guide for reflexive practices to make the sciences more inclusive and just. Ecosphere, 16(4). Portico. https://doi.org/10.1002/ecs2.70168", + "auto_ref": true + }, + { + "doi": "10.1007/s40037-018-0412-2", + "apa": "Reid, A.-M., Brown, J. M., Smith, J. M., Cope, A. C., & Jamieson, S. (2018). Ethical dilemmas and reflexivity in qualitative research. Perspectives on Medical Education, 7(2), 69–75. https://doi.org/10.1007/s40037-018-0412-2", + "auto_ref": true + }, + { + "doi": "10.1007/s13194-020-00324-7", + "apa": "Field, S. M., & Derksen, M. (2020). Experimenter as automaton; experimenter as human: exploring the position of the researcher in scientific research. European Journal for Philosophy of Science, 11(1). https://doi.org/10.1007/s13194-020-00324-7", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/ga5fb_v1", + "apa": "Field, S. M., & Pownall, M. (2025). Subjectivity is a Feature, not a Flaw: A Call to Unsilence the Human Element in Science. https://doi.org/10.31219/osf.io/ga5fb_v1", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/6z9c3_v1", + "apa": "Field, S. M. (2025). Open With Care! Consent, Context, and Co-production in Open Qualitative Research. https://doi.org/10.31219/osf.io/6z9c3_v1", + "auto_ref": true + }, + { + "doi": "10.1080/02615470601118662", + "apa": "Fook, J., & Askeland, G. A. (2007). Challenges of Critical Reflection: ‘Nothing Ventured, Nothing Gained.’ Social Work Education, 26(5), 520–533. https://doi.org/10.1080/02615470601118662", + "auto_ref": true + }, + { + "doi": "10.1080/14623943.2015.1134471", + "apa": "Goldblatt, H., & Band-Winterstein, T. (2016). From understanding to insight: using reflexivity to promote students’ learning of qualitative research. Reflective Practice, 17(2), 100–113. https://doi.org/10.1080/14623943.2015.1134471", + "auto_ref": true + }, + { + "doi": "10.1177/1077800403262360", + "apa": "Guillemin, M., & Gillam, L. (2004). Ethics, Reflexivity, and “Ethically Important Moments” in Research. Qualitative Inquiry, 10(2), 261–280. https://doi.org/10.1177/1077800403262360", + "auto_ref": true + }, + { + "doi": "10.1285/i24212113v5i2p63", + "apa": "Hope, E. C., Brugh, C. S., & Nance, A. (2019). In search of a critical stance: Applying qualitative research practices for critical quantitative research in psychology (Version 1.0) [Data set]. University of Salento. https://doi.org/10.1285/I24212113V5I2P63", + "auto_ref": true + }, + { + "doi": "10.1177/1609406919870075", + "apa": "Jacobson, D., & Mustafa, N. (2019). Social Identity Map: A Reflexivity Tool for Practicing Explicit Positionality in Critical Qualitative Research. International Journal of Qualitative Methods, 18. https://doi.org/10.1177/1609406919870075", + "auto_ref": true + }, + { + "doi": "10.1111/spc3.12735", + "apa": "Jamieson, M. K., Govaart, G. H., & Pownall, M. (2023). Reflexivity in quantitative research: A rationale and beginner’s guide. Social and Personality Psychology Compass, 17(4). Portico. https://doi.org/10.1111/spc3.12735", + "auto_ref": true + }, + { + "doi": "10.1017/S1537592720004703", + "apa": "Kapiszewski, D., & Wood, E. J. (2021). Ethics, Epistemology, and Openness in Research with Human Participants. Perspectives on Politics, 20(3), 948–964. https://doi.org/10.1017/s1537592720004703", + "auto_ref": true + }, + { + "doi": "10.1080/14780887.2017.1400144", + "apa": "Lazard, L., & McAvoy, J. (2017). Doing reflexivity in psychological research: What’s the point? What’s the practice? Qualitative Research in Psychology, 17(2), 159–177. https://doi.org/10.1080/14780887.2017.1400144", + "auto_ref": true + }, + { + "doi": "10.1177/1609406916681005", + "apa": "Mao, L., Mian Akram, A., Chovanec, D., & Underwood, M. L. (2016). Embracing the Spiral. International Journal of Qualitative Methods, 15(1). https://doi.org/10.1177/1609406916681005", + "auto_ref": true + }, + { + "doi": "10.1615/jwomenminorscieneng.2022044277", + "apa": "Martin, J. P., Desing, R., & Borrego, M. (2022). POSITIONALITY STATEMENTS ARE JUST THE TIP OF THE ICEBERG: MOVING TOWARDS A REFLEXIVE PROCESS. Journal of Women and Minorities in Science and Engineering, 28(4), v–vii. https://doi.org/10.1615/jwomenminorscieneng.2022044277", + "auto_ref": true + }, + { + "doi": "", + "apa": "Pham, J., Perry-Wilson, T., Holmes, K., Schroeder, G., Reyes, A., & Pollok, M. (2025). The power of decolonizing research practices. The Professional Counselor, 15(1). https://tpcjournal.nbcc.org/the-power-of-decolonizing-research-practices", + "auto_ref": false + }, + { + "doi": "", + "apa": "Prosser, A., (2025). Unheard, or unspoken? How listening to qualitative researcher voices will shape the future of open research [Plenary slides]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Plenary session). Community of Practice for Naturally Occurring Data. https://osf.io/vnm7p", + "auto_ref": false + }, + { + "doi": "", + "apa": "Prosser, A., (2025). Unheard, or unspoken? How listening to qualitative researcher voices will shape the future of open research [Video]. In Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Plenary session). Community of Practice for Naturally Occurring Data. https://osf.io/pxcy5", + "auto_ref": false + }, + { + "doi": "10.1007/s40037-018-0412-2", + "apa": "Reid, A.-M., Brown, J. M., Smith, J. M., Cope, A. C., & Jamieson, S. (2018). Ethical dilemmas and reflexivity in qualitative research. Perspectives on Medical Education, 7(2), 69–75. https://doi.org/10.1007/s40037-018-0412-2", + "auto_ref": true + }, + { + "doi": "10.36850/mr7", + "apa": "Steltenpohl, C. N., Lustick, H., Meyer, M. S., Lee, L. E., Stegenga, S. M., Standiford Reyes, L., & Renbarger, R. L. (2023). Rethinking Transparency and Rigor from a Qualitative Open Science Perspective. Journal of Trial and Error, 4(1), 47–59. KB. https://doi.org/10.36850/mr7", + "auto_ref": true + } + ] + }, + { + "name": "Replication research", + "description": "Replication is a somewhat controversial topic within qualitative circles. Some researchers (e.g., Makel et al., 2022) argue that replication is useful for supporting transparency and intentionality, examining transferability of findings, and evaluating connections between reflexivity and research findings. Other researchers (e.g., Pownall, 2022) argue that before someone engages in replication of qualitative studies, they should critically examine how, why, and when it would make sense to do so, given differences in epistemologies and ontologies among qualitative researchers.", + "publications": [ + { + "doi": "10.31235/osf.io/rbyt6_v1", + "apa": "Bartscherer, S. F., & Reinhart, M. (2025). The (Non)Academic Community Forming around Replications: Mapping the International Open Science space via its Replication Initiatives. https://doi.org/10.31235/osf.io/rbyt6_v1", + "auto_ref": true + }, + { + "doi": "10.31222/osf.io/n5zkw", + "apa": "Cole, N. L., Ulpts, S., Bochynska, A., Kormann, E., Good, M., Leitner, B., & Ross-Hellauer, T. (2024). Reproducibility and replicability of qualitative research: an integrative review of concepts, barriers and enablers. https://doi.org/10.31222/osf.io/n5zkw", + "auto_ref": true + }, + { + "doi": "10.1080/13803611.2021.2022310", + "apa": "Makel, M. C., Meyer, M. S., Simonsen, M. A., Roberts, A. M., & Plucker, J. A. (2022). Replication is relevant to qualitative research. Educational Research and Evaluation, 27(1–2), 215–219. https://doi.org/10.1080/13803611.2021.2022310", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/dwxeg", + "apa": "Pownall, M. (2022). Is replication possible for qualitative research? https://doi.org/10.31234/osf.io/dwxeg", + "auto_ref": true + }, + { + "doi": "10.1080/13803611.2024.2314526", + "apa": "Pownall, M. (2024). Is replication\n possible\n in qualitative research? A response to Makel et al. (2022). Educational Research and Evaluation, 29(1–2), 104–110. https://doi.org/10.1080/13803611.2024.2314526", + "auto_ref": true + }, + { + "doi": "10.1177/0001839219887663", + "apa": "Pratt, M. G., Kaplan, S., & Whittington, R. (2019). Editorial Essay: The Tumult over Transparency: Decoupling Transparency from Replication in Establishing Trustworthy Qualitative Research. Administrative Science Quarterly, 65(1), 1–19. https://doi.org/10.1177/0001839219887663", + "auto_ref": true + }, + { + "doi": "10.36850/mr7", + "apa": "Steltenpohl, C. N., Lustick, H., Meyer, M. S., Lee, L. E., Stegenga, S. M., Standiford Reyes, L., & Renbarger, R. L. (2023). Rethinking Transparency and Rigor from a Qualitative Open Science Perspective. Journal of Trial and Error, 4(1), 47–59. KB. https://doi.org/10.36850/mr7", + "auto_ref": true + } + ] + }, + { + "name": "Secondary data analysis", + "description": "Secondary data analysis of quantitative methods is now prevalent and encouraged across disciplines in order to reduce costs of data collection, whereas the practice for qualitative data has been fraught with controversy that leads to concerns regarding methodological and ethical dilemmas (e.g. identity of the individual). However, depending on the positionality of the individual, it leads to more nuanced meanings that can ensure researchers can learn from one another. This section outlines some of the issues in secondary data analysis and recommendations to address these challenges.", + "publications": [ + { + "doi": "10.1080/13645579.2012.688335", + "apa": "Bishop, L. (2012). Using archived qualitative data for teaching: practical and ethical considerations. International Journal of Social Research Methodology, 15(4), 341–350. https://doi.org/10.1080/13645579.2012.688335", + "auto_ref": true + }, + { + "doi": "", + "apa": "Bishop, L. (2014). Re-using qualitative data: A little evidence, on-going issues and modest reflections. Studia Socjologiczne. 3. 167-176.", + "auto_ref": false + }, + { + "doi": "10.1080/13645570310001640699", + "apa": "FIELDING, N. (2004). Getting the most from archived qualitative data: epistemological, practical and professional obstacles. International Journal of Social Research Methodology, 7(1), 97–104. https://doi.org/10.1080/13645570310001640699", + "auto_ref": true + }, + { + "doi": "10.1177/1744987110381553", + "apa": "Long-Sutehall, T., Sque, M., & Addington-Hall, J. (2010). Secondary analysis of qualitative data: a valuable method for exploring sensitive issues with an elusive population? Journal of Research in Nursing, 16(4), 335–344. https://doi.org/10.1177/1744987110381553", + "auto_ref": true + }, + { + "doi": "10.1177/1473325017700701", + "apa": "Ruggiano, N., & Perry, T. E. (2017). Conducting secondary analysis of qualitative data: Should we, can we, and how? Qualitative Social Work, 18(1), 81–97. https://doi.org/10.1177/1473325017700701", + "auto_ref": true + } + ] + }, + { + "name": "Standards and guidelines for rigorous qualitative research", + "description": "", + "publications": [ + { + "doi": "", + "apa": "Learn about different standards for reporting qualitative research processes and results. It may be helpful to first read Clarke’s (2022) piece on whether generic reporting standards are helpful in the first place.", + "auto_ref": false + }, + { + "doi": "10.1080/14780887.2020.1769238", + "apa": "Braun, V., & Clarke, V. (2020). One size fits all? What counts as quality practice in (reflexive) thematic analysis? Qualitative Research in Psychology, 18(3), 328–352. https://doi.org/10.1080/14780887.2020.1769238", + "auto_ref": true + }, + { + "doi": "10.1080/14780887.2021.1995555", + "apa": "Clarke, V. (2021). Navigating the messy swamp of qualitative research: Are generic reporting standards the answer?A review essay of the book Reporting Qualitative Research in Psychology: How to Meet APA Style Journal Article Reporting Standards, Revised Edition, by Heidi M. Levitt, Washington, DC, American Psychological Association, 2020, 173pp., $29.99 (paperback), ISBN: 978-1-4338-3343-4. Qualitative Research in Psychology, 19(4), 1004–1012. https://doi.org/10.1080/14780887.2021.1995555", + "auto_ref": true + }, + { + "doi": "10.1207/s15430421tip3903_2", + "apa": "Creswell, J. W., & Miller, D. L. (2000). Determining Validity in Qualitative Inquiry. Theory Into Practice, 39(3), 124–130. https://doi.org/10.1207/s15430421tip3903_2", + "auto_ref": true + }, + { + "doi": "10.1177/104973230201200211", + "apa": "Davies, D., & Dodd, J. (2002). Qualitative Research and the Question of Rigor. Qualitative Health Research, 12(2), 279–289. https://doi.org/10.1177/104973230201200211", + "auto_ref": true + }, + { + "doi": "10.5281/zenodo.2673016", + "apa": "Duckles, B. M., & Steeves, V. (2019). Qualitative Research Using Open Tools. https://doi.org/10.5281/ZENODO.2673016", + "auto_ref": true + }, + { + "doi": "10.31235/osf.io/wc35g", + "apa": "Frohwirth, L., Karcher, S., & Lever, T. A. (2023). A Transparency Checklist for Qualitative Research. https://doi.org/10.31235/osf.io/wc35g", + "auto_ref": true + }, + { + "doi": "", + "apa": "Huang, R. (2016). RQDA: R-based qualitative data analysis (Version 0.2-8) [Computer software]. R Project. http://rqda.r-forge.r-project.org/", + "auto_ref": false + }, + { + "doi": "10.5688/ajpe7120", + "apa": "Johnson, J. L., Adkins, D., & Chauvin, S. (2020). A Review of the Quality Indicators of Rigor in Qualitative Research. American Journal of Pharmaceutical Education, 84(1), 7120. https://doi.org/10.5688/ajpe7120", + "auto_ref": true + }, + { + "doi": "10.1037/amp0000151", + "apa": "Levitt, H. M., Bamberg, M., Creswell, J. W., Frost, D. M., Josselson, R., & Suárez-Orozco, C. (2018). Journal article reporting standards for qualitative primary, qualitative meta-analytic, and mixed methods research in psychology: The APA Publications and Communications Board task force report. American Psychologist, 73(1), 26–46. https://doi.org/10.1037/amp0000151", + "auto_ref": true + }, + { + "doi": "", + "apa": "Levitt, H. M. (2020). Reporting qualitative research in psychology: How to meet APA style journal article reporting standards. American Psychological Association.", + "auto_ref": false + }, + { + "doi": "10.1002/ev.1427", + "apa": "Lincoln, Y. S., & Guba, E. G. (1986). But is it rigorous? Trustworthiness and authenticity in naturalistic evaluation. New Directions for Program Evaluation, 1986(30), 73–84. Portico. https://doi.org/10.1002/ev.1427", + "auto_ref": true + }, + { + "doi": "10.1016/S0140-6736(01)05627-6", + "apa": "Malterud, K. (2001). Qualitative research: standards, challenges, and guidelines. The Lancet, 358(9280), 483–488. https://doi.org/10.1016/s0140-6736(01)05627-6", + "auto_ref": true + }, + { + "doi": "10.1046/j.1365-2648.2003.02509.x", + "apa": "Mill, J. E., & Ogilvie, L. D. (2003). Establishing methodological rigour in international qualitative nursing research: a case study from Ghana. Journal of Advanced Nursing, 41(1), 80–87. Portico. https://doi.org/10.1046/j.1365-2648.2003.02509.x", + "auto_ref": true + }, + { + "doi": "10.3233/EFI-190261", + "apa": "Schindler, C., Veja, C., Hocker, J., Kminek, H., & Meier, M. (2020). Collaborative open analysis in a qualitative research environment. Education for Information, 36(3), 247–261. https://doi.org/10.3233/efi-190261", + "auto_ref": true + }, + { + "doi": "10.1111/bjhp.12393", + "apa": "Shaw, R. L., Bishop, F. L., Horwood, J., Chilcot, J., & Arden, M. A. (2019). Enhancing the quality and transparency of qualitative research methods in health psychology. British Journal of Health Psychology, 24(4), 739–745. Portico. https://doi.org/10.1111/bjhp.12393", + "auto_ref": true + }, + { + "doi": "10.1080/2159676X.2021.1901138", + "apa": "Tamminen, K. A., Bundon, A., Smith, B., McDonough, M. H., Poucher, Z. A., & Atkinson, M. (2021). Considerations for making informed choices about engaging in open qualitative research. Qualitative Research in Sport, Exercise and Health, 13(5), 864–886. https://doi.org/10.1080/2159676x.2021.1901138", + "auto_ref": true + }, + { + "doi": "", + "apa": "Kapiszewski, D., Karcher S., SSRC & Qualitative Data Repository. (n.d.). Managing qualitative social science data [Online course]. Social Science Research Council. https://managing-qualitative-data.org", + "auto_ref": false + }, + { + "doi": "", + "apa": "Groot-Sluijsmans, B., & van Acht, F. (2025). Qualitative participatory research and citizen science: A workshop on quality and ethics of community-based collaborations in research practice [Workshop]. Qualitative Open Science: Challenges, Opportunities, Tensions, and Synergies (Symposium). Community of Practice for Naturally Occurring Data. https://osf.io/xbqm3", + "auto_ref": false + }, + { + "doi": "10.1037/mot0000398", + "apa": "Harmon-Jones, E., Harmon-Jones, C., Amodio, D. M., Gable, P. A., & Schmeichel, B. J. (2025). Valid replications require valid methods: Recommendations for best methodological practices with lab experiments. Motivation Science, 11(3), 235–245. https://doi.org/10.1037/mot0000398", + "auto_ref": true + } + ] + }, + { + "name": "Transparency in qualitative research", + "description": "Transparency in qualitative research tends to focus not only on transparency towards other researchers and/or funders, but also the communities with which they work. Rather than focusing on transparency insofar as it leads to reproducibility, qualitative researchers tend to focus on transparency insofar as it allows readers to understand the context under which research was done and allow them to come to their own conclusions about the extent to which research findings are logical, reliable, and generalizable.", + "publications": [ + { + "doi": "10.1093/joc/jqab026", + "apa": "Humphreys, L., Lewis, N. A., Sender, K., & Won, A. S. (2021). Integrating Qualitative Methods and Open Science: Five Principles for More Trustworthy Research*. Journal of Communication. https://doi.org/10.1093/joc/jqab026", + "auto_ref": true + }, + { + "doi": "10.1017/S1537592720001164", + "apa": "Jacobs, A. M., Büthe, T., Arjona, A., Arriola, L. R., Bellin, E., Bennett, A., Björkman, L., Bleich, E., Elkins, Z., Fairfield, T., Gaikwad, N., Greitens, S. C., Hawkesworth, M., Herrera, V., Herrera, Y. M., Johnson, K. S., Karakoç, E., Koivu, K., Kreuzer, M., … Yashar, D. J. (2021). The Qualitative Transparency Deliberations: Insights and Implications. Perspectives on Politics, 19(1), 171–208. https://doi.org/10.1017/s1537592720001164", + "auto_ref": true + }, + { + "doi": "10.1017/S1049096520000955", + "apa": "Kapiszewski, D., & Karcher, S. (2020). Transparency in Practice in Qualitative Research. PS: Political Science & Politics, 54(2), 285–291. https://doi.org/10.1017/s1049096520000955", + "auto_ref": true + }, + { + "doi": "10.1017/S1537592720004703", + "apa": "Kapiszewski, D., & Wood, E. J. (2021). Ethics, Epistemology, and Openness in Research with Human Participants. Perspectives on Politics, 20(3), 948–964. https://doi.org/10.1017/s1537592720004703", + "auto_ref": true + }, + { + "doi": "10.4135/9781526421036", + "apa": "Denzin, Norman. (2020). https://doi.org/10.4135/9781526421036", + "auto_ref": true + }, + { + "doi": "", + "apa": "Prosser, A. M., Brown, O., Augustine, G., & Ellis, D. (2024). It’s time to join the conversation: Visions of the future for qualitative transparency and openness in management and organisation studies. SocArXiv. https://osf.io/preprints/socarxiv/ntf73", + "auto_ref": false + }, + { + "doi": "10.3233/EFI-190261", + "apa": "Schindler, C., Veja, C., Hocker, J., Kminek, H., & Meier, M. (2020). Collaborative open analysis in a qualitative research environment. Education for Information, 36(3), 247–261. https://doi.org/10.3233/efi-190261", + "auto_ref": true + }, + { + "doi": "10.1111/bjhp.12393", + "apa": "Shaw, R. L., Bishop, F. L., Horwood, J., Chilcot, J., & Arden, M. A. (2019). Enhancing the quality and transparency of qualitative research methods in health psychology. British Journal of Health Psychology, 24(4), 739–745. Portico. https://doi.org/10.1111/bjhp.12393", + "auto_ref": true + }, + { + "doi": "", + "apa": "Stahl, N. A., & King, J. R. (2020). Expanding approaches for research: Understanding and using trustworthiness in qualitative research. Journal of Developmental Education, 44(1), 26–28. https://files.eric.ed.gov/fulltext/EJ1320570.pdf", + "auto_ref": false + }, + { + "doi": "10.36850/mr7", + "apa": "Steltenpohl, C. N., Lustick, H., Meyer, M. S., Lee, L. E., Stegenga, S. M., Standiford Reyes, L., & Renbarger, R. L. (2023). Rethinking Transparency and Rigor from a Qualitative Open Science Perspective. Journal of Trial and Error, 4(1), 47–59. KB. https://doi.org/10.36850/mr7", + "auto_ref": true + } + ] + } + ] + }, + { + "number": 11, + "name": "Research Integrity", + "description": "Research Integrity (RI) encompasses the moral and professional standards that ensure research is trustworthy, transparent, and ethical from inception to publication​. Traditionally, RI efforts have centered on preventing misconduct—the blatant fabrication, falsification, or plagiarism (FFP) that betrays the core of science. Modern perspectives, however, advocate a holistic vision: cultivating a culture of responsible, equitable, and open research practices that goes beyond avoiding misconduct to actively promoting excellence and fairness. Supervision, mentorship, and everyday collegial relations have an important part in cultivating a culture of research integrity and shaping what “good practice” looks like in labs and teams to new researchers. This includes how power dynamics, authorship, and credit are negotiated. Institutions matter too, policies, incentives, workload, and leadership either enable or erode integrity. RI is intrinsically linked with the Open Science movement. Both strive to make research more transparent and accountable, thereby strengthening credibility and public trust​. Open Science initiatives (e.g. data sharing, preregistration, open access) can make misconduct easier to detect and discourage, while fostering norms of honesty and rigor. Conversely, RI provides the ethical foundation for openness – emphasizing values like honesty, accountability, respect, and fairness that guide how openness is pursued. By making research integrity “possible, easy, normative, and rewarding” (Haven et al., 2022)​, institutions and communities create an environment where ethical, inclusive, and rigorous research thrives. Ultimately, RI is about more than rule-following; it is about embedding integrity as a fundamental ethos of research design, conduct, and dissemination – ensuring science advances knowledge and the public good in tandem.[as]", + "sub_clusters": [ + { + "name": "Principles and Frameworks of Research Integrity", + "description": "This sub-cluster covers the core principles, codes, and global frameworks that define research integrity. It introduces the fundamental values (e.g. honesty, rigor, transparency, accountability, respect) that underpin responsible science​. Key international statements and guidelines – such as the Singapore Statement (2010) and ALLEA’s European Code of Conduct (2017) – articulate universal norms and responsibilities for researchers. They emphasize that integrity spans all stages of research, from study design and data collection to authorship and peer review. Foundational documents (e.g. the U.S. National Academies 2017 report) situate RI in a broader context, calling for supportive research environments and institutional policies that foster ethical behavior. By studying these frameworks, one gains insight into how core values (e.g., honesty, transparency, accountability, respect) are operationalized into norms and good research practice across the research cycle. Explicitly articulated in the Netherlands Code of Conduct and agreed upon by the global research community “doing the right thing” means not only avoiding misconduct but proactively promoting openness, accountability, and social responsibility in science with clear links between specific practices and potential breaches or allegations.", + "publications": [ + { + "doi": "", + "apa": "ALLEA – All European Academies. (2017). The European Code of Conduct for Research Integrity (Revised Edition). – European guidance emphasizing honesty, reliability, respect, and accountability in all research practices.", + "auto_ref": false + }, + { + "doi": "10.1007/978-981-287-098-8", + "apa": "Bretag, T. (Ed.). (2016). Handbook of Academic Integrity. https://doi.org/10.1007/978-981-287-098-8", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2023.2167599", + "apa": "de Ridder, J., Bouter, L., Haven, T., Peels, R., Tijdink, J., & Zeegers, M. P. (2023). In Defense of the Netherlands Code of Conduct for Research Integrity: Response to Radder. Accountability in Research, 30(5), 276–283. https://doi.org/10.1080/08989621.2023.2167599", + "auto_ref": true + }, + { + "doi": "10.31219/osf.io/6z9c3_v1", + "apa": "Field, S. M. (2025). Open With Care! Consent, Context, and Co-production in Open Qualitative Research. https://doi.org/10.31219/osf.io/6z9c3_v1", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-018-0034-4", + "apa": "Forsberg, E.-M., Anthun, F. O., Bailey, S., Birchley, G., Bout, H., Casonato, C., Fuster, G. G., Heinrichs, B., Horbach, S., Jacobsen, I. S., Janssen, J., Kaiser, M., Lerouge, I., van der Meulen, B., de Rijcke, S., Saretzki, T., Sutrop, M., Tazewell, M., Varantola, K., … Zöller, M. (2018). Working with Research Integrity—Guidance for Research Performing Organisations: The Bonn PRINTEGER Statement. Science and Engineering Ethics, 24(4), 1023–1034. https://doi.org/10.1007/s11948-018-0034-4", + "auto_ref": true + }, + { + "doi": "10.1093/scipol/scac067", + "apa": "Hastings, R., Labib, K., Lechner, I., Bouter, L., Widdershoven, G., & Evans, N. (2022). Guidance on research integrity provided by pan-European discipline-specific learned societies: A scoping review. Science and Public Policy, 50(2), 318–335. https://doi.org/10.1093/scipol/scac067", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pbio.3001773", + "apa": "Horbach, S. P. J. M., Bouter, L. M., Gaskell, G., Hiney, M., Kavouras, P., Mejlgaard, N., Allum, N., Aubert Bonn, N., Bendtsen, A.-K., Charitidis, C. A., Claesen, N., Dierickx, K., Domaradzka, A., Elizondo, A. R., Föger, N., Kaltenbrunner, W., Konach, T., Labib, K., Marušić, A., … Tijdink, J. K. (2022). Designing and implementing a research integrity promotion plan: Recommendations for research funders. PLOS Biology, 20(8), e3001773. https://doi.org/10.1371/journal.pbio.3001773", + "auto_ref": true + }, + { + "doi": "10.17026/dans-2cj-nvwu", + "apa": "KNAW, NFU, NWO, TO2-Federatie, Vereniging Hogescholen, & VSNU. (2018). Nederlandse gedragscode wetenschappelijke integriteit [Data set]. Data Archiving and Networked Services (DANS). https://doi.org/10.17026/DANS-2CJ-NVWU", + "auto_ref": true + }, + { + "doi": "10.1111/dewb.12024", + "apa": "Kombe, F., Anunobi, E. N., Tshifugula, N. P., Wassenaar, D., Njadingwe, D., Mwalukore, S., Chinyama, J., Randrianasolo, B., Akindeh, P., Dlamini, P. S., Ramiandrisoa, F. N., & Ranaivo, N. (2013). Promoting Research Integrity in Africa: An African Voice of Concern on Research Misconduct and the Way Forward. Developing World Bioethics, 14(3), 158–166. Portico. https://doi.org/10.1111/dewb.12024", + "auto_ref": true + }, + { + "doi": "10.17226/21896", + "apa": "(2017). Fostering Integrity in Research. https://doi.org/10.17226/21896", + "auto_ref": true + }, + { + "doi": "10.1186/s41073-019-0076-4", + "apa": "Peels, R., de Ridder, J., Haven, T., & Bouter, L. (2019). Value pluralism in research integrity. Research Integrity and Peer Review, 4(1). https://doi.org/10.1186/s41073-019-0076-4", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2014.1002608", + "apa": "Resnik, D. B., & Elliott, K. C. (2015). The Ethical Challenges of Socially Responsible Science. Accountability in Research, 23(1), 31–46. https://doi.org/10.1080/08989621.2014.1002608", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-024-00467-3", + "apa": "Reyes Elizondo, A., & Kaltenbrunner, W. (2024). Navigating the Science System: Research Integrity and Academic Survival Strategies. Science and Engineering Ethics, 30(2). https://doi.org/10.1007/s11948-024-00467-3", + "auto_ref": true + }, + { + "doi": "", + "apa": "Singapore Statement on Research Integrity (2010). Singapore: 2nd World Conference on Research Integrity. – Landmark statement outlining 4 principles and 14 responsibilities for ethical research conduct.", + "auto_ref": false + }, + { + "doi": "10.1007/pl00022268", + "apa": "Steneck, N. H. (2006). Fostering integrity in research: Definitions, current knowledge, and future directions. Science and Engineering Ethics, 12(1), 53–74. https://doi.org/10.1007/pl00022268", + "auto_ref": true + }, + { + "doi": "10.1007/s10805-019-09342-4", + "apa": "Tauginienė, L., Gaižauskaitė, I., Razi, S., Glendinning, I., Sivasubramaniam, S., Marino, F., Cosentino, M., Anohina-Naumeca, A., & Kravjar, J. (2019). Enhancing the Taxonomies Relating to Academic Integrity and Misconduct. Journal of Academic Ethics, 17(4), 345–361. https://doi.org/10.1007/s10805-019-09342-4", + "auto_ref": true + }, + { + "doi": "10.1177/15562646211018916", + "apa": "Tijdink, J. K., Horbach, S. P. J. M., Nuijten, M. B., & O’Neill, G. (2021). Towards a Research Agenda for Promoting Responsible Research Practices. Journal of Empirical Research on Human Research Ethics, 16(4), 450–460. https://doi.org/10.1177/15562646211018916", + "auto_ref": true + }, + { + "doi": "", + "apa": "UNESCO. (2017). Recommendation on Science and Scientific Researchers. Paris: UNESCO. https://unesdoc.unesco.org/ark:/48223/pf0000263618 – United Nations guidelines stressing researchers’ responsibilities to society, the need for training, and the importance of an inclusive, ethical research system globally.", + "auto_ref": false + }, + { + "doi": "", + "apa": "UNESCO. (2023). UNESCO Recommendation on Open Science — About open science. https://www.unesco.org/en/open-science/about – Both OS and RI principles aim to make research transparent and accountable. Open Science helps deter and detect misconduct and normalizes rigor. Research Integrity provides the ethical base, guiding how openness is pursued;", + "auto_ref": false + }, + { + "doi": "", + "apa": "World Conference on Research Integrity. (2013). Montreal Statement on Research Integrity in Cross-Boundary Research Collaborations. – Guidelines to ensure integrity, fairness, and equity in international and interdisciplinary research partnerships.", + "auto_ref": false + } + ] + }, + { + "name": "Research Misconduct: Fabrication, Falsification, Plagiarism", + "description": "This sub-cluster focuses on the “cardinal sins” of research – intentional acts that grossly violate integrity. Research misconduct is formally defined (in many policies) as fabrication (making up data or results), falsification (manipulating research processes or data), and plagiarism (using others’ ideas or words without credit). These actions undermine the very foundation of science by injecting falsehoods and eroding trust. Students explore famous misconduct cases and their repercussions, as well as studies on how frequently scientists admit to misbehavior. Surveys suggest blatant misconduct is rare but not vanishingly so (on the order of 2%–4% of researchers, depending on field, have admitted to Fabrication, Fallisfication and Plagiarism (FFP) (Bouter, 2024), with higher percentages witnessing or suspecting it in others​ (Bouter, 2024)). Beyond statistics, readings discuss the causes and risk factors for misconduct – e.g. extreme publication pressure or inadequate oversight – and the systems in place to detect and deter FFP (institutional investigations, whistleblower protections, and sanctions like retractions). This sub-cluster sets a cautionary foundation: understanding what not to do in research, why such behavior occurs, and how the scientific community responds when the worst breaches of integrity come to light.", + "publications": [ + { + "doi": "10.1080/08989621.2023.2189010", + "apa": "Bouter, L. (2023). Why research integrity matters and how it can be improved. Accountability in Research, 31(8), 1277–1286. https://doi.org/10.1080/08989621.2023.2189010", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0005738", + "apa": "Fanelli, D. (2009). How Many Scientists Fabricate and Falsify Research? A Systematic Review and Meta-Analysis of Survey Data. PLoS ONE, 4(5), e5738. https://doi.org/10.1371/journal.pone.0005738", + "auto_ref": true + }, + { + "doi": "10.1007/s10838-021-09555-5", + "apa": "Haven, T., & van Woudenberg, R. (2021). Explanations of Research Misconduct, and How They Hang Together. Journal for General Philosophy of Science, 52(4), 543–561. https://doi.org/10.1007/s10838-021-09555-5", + "auto_ref": true + }, + { + "doi": "10.1093/scipol/scy068", + "apa": "Horbach, S. P. J. M., Breit, E., & Mamelund, S.-E. (2018). Organisational responses to alleged scientific misconduct: Sensemaking, sensegiving, and sensehiding. Science and Public Policy, 46(3), 415–429. https://doi.org/10.1093/scipol/scy068", + "auto_ref": true + }, + { + "doi": "10.1038/435737a", + "apa": "Martinson, B. C., Anderson, M. S., & de Vries, R. (2005). Scientists behaving badly. Nature, 435(7043), 737–738. https://doi.org/10.1038/435737a", + "auto_ref": true + }, + { + "doi": "10.1177/1745691612460687", + "apa": "Stroebe, W., Postmes, T., & Spears, R. (2012). Scientific Misconduct and the Myth of Self-Correction in Science. Perspectives on Psychological Science, 7(6), 670–688. https://doi.org/10.1177/1745691612460687", + "auto_ref": true + }, + { + "doi": "10.1038/453980a", + "apa": "Titus, S. L., Wells, J. A., & Rhoades, L. J. (2008). Repairing research integrity. Nature, 453(7198), 980–982. https://doi.org/10.1038/453980a", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-021-00314-9", + "apa": "Xie, Y., Wang, K., & Kong, Y. (2021). Prevalence of Research Misconduct and Questionable Research Practices: A Systematic Review and Meta-Analysis. Science and Engineering Ethics, 27(4). https://doi.org/10.1007/s11948-021-00314-9", + "auto_ref": true + } + ] + }, + { + "name": "Questionable Research Practices and Responsible Research Practices", + "description": "Not all integrity problems are as black-and-white as FFP. This sub-cluster examines the gray zone of Questionable Research Practices (QRPs) – behaviors that don’t blatantly falsify data, yet still deviate from good scientific practice and can undermine credibility. Examples include p-hacking (tuning analyses until results are significant), HARKing (Hypothesizing After Results are Known), selective reporting of only positive outcomes, incomplete methods reporting, inadequate data management, or sidestepping human subjects protocols. Studies have revealed alarmingly high rates of QRPs: for instance, a survey in psychology found over half of researchers admitted to at least one QRP such as selectively reporting studies or unexpected analyses​ - (Bouter, 2024). QRPs collectively contribute to the reproducibility crisis by inflating false-positive findings and distorting the literature​ - (Bouter, 2024). To address this, the research community has begun promoting Responsible Research Practices (RRPs) – methodological reforms and Open Science techniques designed to curb QRPs. These include preregistration of study plans (to prevent HARKing), sharing data and code (to increase transparency), publishing replication studies and null results, and using reporting guidelines. Embracing RRPs can make honest, thorough research the path of least resistance. In sum, this sub-cluster highlights the continuum between outright misconduct and ideal practices, stressing that everyday decisions in analysis and reporting are central to research integrity.", + "publications": [ + { + "doi": "10.1007/978-981-287-098-8", + "apa": "Bretag, T. (Ed.). (2016). Handbook of Academic Integrity. https://doi.org/10.1007/978-981-287-098-8", + "auto_ref": true + }, + { + "doi": "10.31234/osf.io/74r2n_v1", + "apa": "Fillon, A. A., Michaelides, M., Gopalakrishna, G., Es-Sadki, N., & Notten, A. (2024). Prevalence of questionable research practices: A survey among academic researchers in Cypriot and Greek institutions, Registered Report Stage 1. https://doi.org/10.31234/osf.io/74r2n_v1", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0263023", + "apa": "Gopalakrishna, G., ter Riet, G., Vink, G., Stoop, I., Wicherts, J. M., & Bouter, L. M. (2022). Prevalence of questionable research practices, research misconduct and their potential explanatory factors: A survey among academic researchers in The Netherlands. PLOS ONE, 17(2), e0263023. https://doi.org/10.1371/journal.pone.0263023", + "auto_ref": true + }, + { + "doi": "10.12688/f1000research.110664.2", + "apa": "Gopalakrishna, G., Wicherts, J. M., Vink, G., Stoop, I., van den Akker, O. R., ter Riet, G., & Bouter, L. M. (2022). Prevalence of responsible research practices among academics in The Netherlands. F1000Research, 11, 471. https://doi.org/10.12688/f1000research.110664.2", + "auto_ref": true + }, + { + "doi": "10.1186/s13104-022-06169-y", + "apa": "Haven, T., Gopalakrishna, G., Tijdink, J., van der Schot, D., & Bouter, L. (2022). Promoting trust in research and researchers: How open science and research integrity are intertwined. BMC Research Notes, 15(1). https://doi.org/10.1186/s13104-022-06169-y", + "auto_ref": true + }, + { + "doi": "10.1186/s41073-021-00110-w", + "apa": "Haven, T., Tijdink, J., Martinson, B., Bouter, L., & Oort, F. (2021). Explaining variance in perceived research misbehavior: results from a survey among academic researchers in Amsterdam. Research Integrity and Peer Review, 6(1). https://doi.org/10.1186/s41073-021-00110-w", + "auto_ref": true + }, + { + "doi": "10.1016/j.respol.2017.09.004", + "apa": "Horbach, S. P. J. M. (Serge), & Halffman, W. (Willem). (2019). The extent and causes of academic text recycling or ‘self-plagiarism.’ Research Policy, 48(2), 492–502. https://doi.org/10.1016/j.respol.2017.09.004", + "auto_ref": true + }, + { + "doi": "10.1177/0956797611430953", + "apa": "John, L. K., Loewenstein, G., & Prelec, D. (2012). Measuring the Prevalence of Questionable Research Practices With Incentives for Truth Telling. Psychological Science, 23(5), 524–532. https://doi.org/10.1177/0956797611430953", + "auto_ref": true + }, + { + "doi": "10.1177/25152459241296397", + "apa": "Lengersdorff, L. L., & Lamm, C. (2025). With Low Power Comes Low Credibility? Toward a Principled Critique of Results From Underpowered Tests. Advances in Methods and Practices in Psychological Science, 8(1). https://doi.org/10.1177/25152459241296397", + "auto_ref": true + }, + { + "doi": "10.1126/science.aab2374", + "apa": "Nosek, B. A., Alter, G., Banks, G. C., Borsboom, D., Bowman, S. D., Breckler, S. J., Buck, S., Chambers, C. D., Chin, G., Christensen, G., Contestabile, M., Dafoe, A., Eich, E., Freese, J., Glennerster, R., Goroff, D., Green, D. P., Hesse, B., Humphreys, M., … Yarkoni, T. (2015). Promoting an open research culture. Science, 348(6242), 1422–1425. https://doi.org/10.1126/science.aab2374", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-024-00467-3", + "apa": "Reyes Elizondo, A., & Kaltenbrunner, W. (2024). Navigating the Science System: Research Integrity and Academic Survival Strategies. Science and Engineering Ethics, 30(2). https://doi.org/10.1007/s11948-024-00467-3", + "auto_ref": true + }, + { + "doi": "", + "apa": "SOPs4RI. (n.d.). Dealing with breaches of research integrity. https://sops4ri.eu/tool_category/breaches/ - A curated SOPs4RI toolbox category offering practical policies and templates for handling breaches of research integrity.", + "auto_ref": false + }, + { + "doi": "10.1177/25152459211007467", + "apa": "Scheel, A. M., Schijen, M. R. M. J., & Lakens, D. (2021). An Excess of Positive Results: Comparing the Standard Psychology Literature With Registered Reports. Advances in Methods and Practices in Psychological Science, 4(2). https://doi.org/10.1177/25152459211007467", + "auto_ref": true + }, + { + "doi": "10.1177/0956797611417632", + "apa": "Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011). False-Positive Psychology. Psychological Science, 22(11), 1359–1366. https://doi.org/10.1177/0956797611417632", + "auto_ref": true + } + ] + }, + { + "name": "Research Culture, Incentives, and Institutional Responsibilities", + "description": "Research integrity is not upheld by individual virtue alone – the culture and incentive structures of academia play a decisive role. This sub-cluster examines how funding, publishing, and career advancement pressures can either encourage integrity or inadvertently foster misconduct/QRPs. A “publish or perish” climate, hypercompetition for grants, and evaluation systems focused on quantity over quality (e.g. rewarding scientists for high-impact publications, citations, and impact factors) can create perverse incentives​ (Bouter, 2024). Such pressures may tempt researchers toward sloppy or dishonest practices to secure positive findings and prestige​ (Bouter, 2024). Crucially, this sub-cluster highlights reforms aimed at aligning incentives with integrity: initiatives like the San Francisco Declaration on Research Assessment (DORA) and Leiden Manifesto call for valuing rigorous methods and openness over simplistic metrics. The Hong Kong Principles (2019) advocate evaluating researchers on transparency, collaboration, and reliability rather than just output count. Institutions and funders are beginning to adopt policies (e.g. random audits, mentoring programs, or even grant lotteries) to promote a healthier research climate. By understanding these dynamics, students appreciate that sustaining RI requires top-down support: universities, journals, and funders must cultivate an environment where ethical, careful science is the most rewarded and celebrated science.", + "publications": [ + { + "doi": "10.12688/f1000research.128733.1", + "apa": "Allum, N., Reid, A., Bidoglia, M., Gaskell, G., Aubert-Bonn, N., Buljan, I., Fuglsang, S., Horbach, S., Kavouras, P., Marušić, A., Mejlgaard, N., Pizzolato, D., Roje, R., Tijdink, J., & Veltri, G. (2023). Researchers on research integrity: a survey of European and American researchers. F1000Research, 12, 187. https://doi.org/10.12688/f1000research.128733.1", + "auto_ref": true + }, + { + "doi": "10.1038/525025a", + "apa": "Begley, C. G., Buchan, A. M., & Dirnagl, U. (2015). Robust research: Institutions must do their part for reproducibility. Nature, 525(7567), 25–27. https://doi.org/10.1038/525025a", + "auto_ref": true + }, + { + "doi": "10.1007/978-981-287-098-8", + "apa": "Bretag, T. (Ed.). (2016). Handbook of Academic Integrity. https://doi.org/10.1007/978-981-287-098-8", + "auto_ref": true + }, + { + "doi": "10.1089/ees.2016.0223", + "apa": "Edwards, M. A., & Roy, S. (2017). Academic Research in the 21st Century: Maintaining Scientific Integrity in a Climate of Perverse Incentives and Hypercompetition. Environmental Engineering Science, 34(1), 51–61. https://doi.org/10.1089/ees.2016.0223", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-018-0034-4", + "apa": "Forsberg, E.-M., Anthun, F. O., Bailey, S., Birchley, G., Bout, H., Casonato, C., Fuster, G. G., Heinrichs, B., Horbach, S., Jacobsen, I. S., Janssen, J., Kaiser, M., Lerouge, I., van der Meulen, B., de Rijcke, S., Saretzki, T., Sutrop, M., Tazewell, M., Varantola, K., … Zöller, M. (2018). Working with Research Integrity—Guidance for Research Performing Organisations: The Bonn PRINTEGER Statement. Science and Engineering Ethics, 24(4), 1023–1034. https://doi.org/10.1007/s11948-018-0034-4", + "auto_ref": true + }, + { + "doi": "10.1007/s11186-025-09614-6", + "apa": "Gelman, A., & Higgs, M. (2025). Interrogating the “cargo cult science” metaphor. Theory and Society, 54(2), 197–207. https://doi.org/10.1007/s11186-025-09614-6", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0217931", + "apa": "Haven, T. L., Bouter, L. M., Smulders, Y. M., & Tijdink, J. K. (2019). Perceived publication pressure in Amsterdam: Survey of all disciplinary fields and academic ranks. PLOS ONE, 14(6), e0217931. https://doi.org/10.1371/journal.pone.0217931", + "auto_ref": true + }, + { + "doi": "10.1186/s41073-019-0066-6", + "apa": "Haven, T. L., de Goede, M. E. E., Tijdink, J. K., & Oort, F. J. (2019). Personally perceived publication pressure: revising the Publication Pressure Questionnaire (PPQ) by using work stress models. Research Integrity and Peer Review, 4(1). https://doi.org/10.1186/s41073-019-0066-6", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-020-00256-8", + "apa": "Haven, T., Pasman, H. R., Widdershoven, G., Bouter, L., & Tijdink, J. (2020). Researchers’ Perceptions of a Responsible Research Climate: A Multi Focus Group Study. Science and Engineering Ethics, 26(6), 3017–3036. https://doi.org/10.1007/s11948-020-00256-8", + "auto_ref": true + }, + { + "doi": "10.1186/s41073-021-00110-w", + "apa": "Haven, T., Tijdink, J., Martinson, B., Bouter, L., & Oort, F. (2021). Explaining variance in perceived research misbehavior: results from a survey among academic researchers in Amsterdam. Research Integrity and Peer Review, 6(1). https://doi.org/10.1186/s41073-021-00110-w", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0210599", + "apa": "Haven, T. L., Tijdink, J. K., Martinson, B. C., & Bouter, L. M. (2019). Perceptions of research integrity climate differ between academic ranks and disciplinary fields: Results from a survey among academic researchers in Amsterdam. PLOS ONE, 14(1), e0210599. https://doi.org/10.1371/journal.pone.0210599", + "auto_ref": true + }, + { + "doi": "10.1038/520429a–", + "apa": "Hicks, D., Wouters, P., Waltman, L., de Rijcke, S., & Rafols, I. (2015). The Leiden Manifesto for research metrics. Nature, 520(7548), 429–431. https://doi.org/10.1038/520429a– Ten principles for responsible research evaluation (e.g. avoid misplaced concreteness of metrics, protect qualitative judgment, account for diversity in fields). A direct response to metric-driven distortions, aiming to realign incentives with integrity and quality.", + "auto_ref": false + }, + { + "doi": "10.1007/s11948-016-9858-y", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2016). Promoting Virtue or Punishing Fraud: Mapping Contrasts in the Language of ‘Scientific Integrity.’ Science and Engineering Ethics, 23(6), 1461–1485. https://doi.org/10.1007/s11948-016-9858-y", + "auto_ref": true + }, + { + "doi": "10.1093/scipol/scad017", + "apa": "Horbach, S. P. J. M., Sørensen, M. P., Allum, N., & Reid, A.-K. (2023). Disentangling the local context—imagined communities and researchers’ sense of belonging. Science and Public Policy, 50(4), 695–706. https://doi.org/10.1093/scipol/scad017", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pbio.3001773", + "apa": "Horbach, S. P. J. M., Bouter, L. M., Gaskell, G., Hiney, M., Kavouras, P., Mejlgaard, N., Allum, N., Aubert Bonn, N., Bendtsen, A.-K., Charitidis, C. A., Claesen, N., Dierickx, K., Domaradzka, A., Elizondo, A. R., Föger, N., Kaltenbrunner, W., Konach, T., Labib, K., Marušić, A., … Tijdink, J. K. (2022). Designing and implementing a research integrity promotion plan: Recommendations for research funders. PLOS Biology, 20(8), e3001773. https://doi.org/10.1371/journal.pbio.3001773", + "auto_ref": true + }, + { + "doi": "10.1093/scipol/scy068", + "apa": "Horbach, S. P. J. M., Breit, E., & Mamelund, S.-E. (2018). Organisational responses to alleged scientific misconduct: Sensemaking, sensegiving, and sensehiding. Science and Public Policy, 46(3), 415–429. https://doi.org/10.1093/scipol/scy068", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-020-00202-8", + "apa": "Horbach, S. P. J. M., Breit, E., Halffman, W., & Mamelund, S.-E. (2020). On the Willingness to Report and the Consequences of Reporting Research Misconduct: The Role of Power Relations. Science and Engineering Ethics, 26(3), 1595–1623. https://doi.org/10.1007/s11948-020-00202-8", + "auto_ref": true + }, + { + "doi": "10.1080/23299460.2024.2414500", + "apa": "Horbach, S. P. J. M., Fishberg, R., Ulpts, S., & Degn, L. (2024). Thou Shalt Not! – How the institutional afterlife of research misconduct scandals shapes research integrity training. Journal of Responsible Innovation, 11(1). https://doi.org/10.1080/23299460.2024.2414500", + "auto_ref": true + }, + { + "doi": "", + "apa": "Horbach, S. P. J. M., Cole, N. L., Kopeinik, S., Leitner, B., Ross-Hellauer, T., & Tijdink, J. (2025). How to get there from here? Barriers and enablers on the road towards reproducibility in research [Manuscript]. OSF. https://osf.io/n28sg/", + "auto_ref": false + }, + { + "doi": "10.1177/20966083251329632", + "apa": "Knibbe, M., de Rijcke, S., & Penders, B. (2025). Care for the soul of science: Equity and virtue in reform and reformation. Cultures of Science, 8(1), 12–23. https://doi.org/10.1177/20966083251329632", + "auto_ref": true + }, + { + "doi": "10.31222/osf.io/zr35u_v1", + "apa": "Crespo López, M. de los Á., Pallise Perello, C., de Ridder, J., & Labib, K. (2025). Open Science as Confused: Contradictory and Conflicting Discourses in Open Science Guidance to Researchers. https://doi.org/10.31222/osf.io/zr35u_v1", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-021-00322-9", + "apa": "Labib, K., Roje, R., Bouter, L., Widdershoven, G., Evans, N., Marušić, A., Mokkink, L., & Tijdink, J. (2021). Important Topics for Fostering Research Integrity by Research Performing and Research Funding Organizations: A Delphi Consensus Study. Science and Engineering Ethics, 27(4). https://doi.org/10.1007/s11948-021-00322-9", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2023.2191192", + "apa": "Labib, K., Tijdink, J., Sijtsma, K., Bouter, L., Evans, N., & Widdershoven, G. (2023). How to combine rules and commitment in fostering research integrity? Accountability in Research, 31(7), 917–943. https://doi.org/10.1080/08989621.2023.2191192", + "auto_ref": true + }, + { + "doi": "10.1186/s13104-022-06030-2", + "apa": "Macleod, M. (2022). Improving the reproducibility and integrity of research: what can different stakeholders contribute? BMC Research Notes, 15(1). https://doi.org/10.1186/s13104-022-06030-2", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0270054", + "apa": "Malički, M., Aalbersberg, Ij. J., Bouter, L., Mulligan, A., & ter Riet, G. (2023). Transparency in conducting and reporting research: A survey of authors, reviewers, and editors across scholarly disciplines. PLOS ONE, 18(3), e0270054. https://doi.org/10.1371/journal.pone.0270054", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-020-02847-8", + "apa": "Mejlgaard, N., Bouter, L. M., Gaskell, G., Kavouras, P., Allum, N., Bendtsen, A.-K., Charitidis, C. A., Claesen, N., Dierickx, K., Domaradzka, A., Reyes Elizondo, A., Foeger, N., Hiney, M., Kaltenbrunner, W., Labib, K., Marušić, A., Sørensen, M. P., Ravn, T., Ščepanović, R., … Veltri, G. A. (2020). Research integrity: nine ways to move from talk to walk. Nature, 586(7829), 358–360. https://doi.org/10.1038/d41586-020-02847-8", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pbio.3000737", + "apa": "Moher, D., Bouter, L., Kleinert, S., Glasziou, P., Sham, M. H., Barbour, V., Coriat, A.-M., Foeger, N., & Dirnagl, U. (2020). The Hong Kong Principles for assessing researchers: Fostering research integrity. PLOS Biology, 18(7), e3000737. https://doi.org/10.1371/journal.pbio.3000737", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-019-01727-0", + "apa": "Research integrity is much more than misconduct. (2019). Nature, 570(7759), 5–5. https://doi.org/10.1038/d41586-019-01727-0", + "auto_ref": true + }, + { + "doi": "10.1242/bio.20135330", + "apa": "Raff, J. W. (2013). The San Francisco Declaration on Research Assessment. Biology Open, 2(6), 533–534. https://doi.org/10.1242/bio.20135330", + "auto_ref": true + }, + { + "doi": "", + "apa": "Ross-Hellauer, Tony & Aubert Bonn, Noémie & Horbach, Serge P. J. M., (2023). Understanding the social and political dimensions of research(er) assessment: Interpretative flexibility and hidden criteria. SocArXiv https://ideas.repec.org/p/osf/socarx/e5uyv_v1.html", + "auto_ref": false + }, + { + "doi": "10.1093/reseval/rvae055", + "apa": "Ross-Hellauer, T., Aubert Bonn, N., & Horbach, S. P. J. M. (2024). Understanding the social and political dimensions of research(er) assessment: evaluative flexibility and hidden criteria in promotion processes at research institutes. Research Evaluation, 33. https://doi.org/10.1093/reseval/rvae055", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-021-00281-1", + "apa": "Ščepanović, R., Labib, K., Buljan, I., Tijdink, J., & Marušić, A. (2021). Practices for Research Integrity Promotion in Research Performing Organisations and Research Funding Organisations: A Scoping Review. Science and Engineering Ethics, 27(1). https://doi.org/10.1007/s11948-021-00281-1", + "auto_ref": true + }, + { + "doi": "10.1177/1556264614552421", + "apa": "Tijdink, J. K., Verbeke, R., & Smulders, Y. M. (2014). Publication Pressure and Scientific Misconduct in Medical Scientists. Journal of Empirical Research on Human Research Ethics, 9(5), 64–71. https://doi.org/10.1177/1556264614552421", + "auto_ref": true + }, + { + "doi": "10.1073/pnas.2401231121", + "apa": "Trueblood, J. S., Allison, D. B., Field, S. M., Fishbach, A., Gaillard, S. D. M., Gigerenzer, G., Holmes, W. R., Lewandowsky, S., Matzke, D., Murphy, M. C., Musslick, S., Popov, V., Roskies, A. L., ter Schure, J., & Teodorescu, A. R. (2025). The misalignment of incentives in academic publishing and implications for journal reform. Proceedings of the National Academy of Sciences, 122(5). https://doi.org/10.1073/pnas.2401231121", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-024-00481-5", + "apa": "van Drimmelen, T., Slagboom, M. N., Reis, R., Bouter, L. M., & van der Steen, J. T. (2024). Decisions, Decisions, Decisions: An Ethnographic Study of Researcher Discretion in Practice. Science and Engineering Ethics, 30(6). https://doi.org/10.1007/s11948-024-00481-5", + "auto_ref": true + }, + { + "doi": "10.1093/scipol/scad052", + "apa": "Wang, J., Halffman, W., & Horbach, S. P. J. M. (2023). Listing quality: Chinese journal lists in incoherent valuation regimes. Science and Public Policy, 51(1), 55–66. https://doi.org/10.1093/scipol/scad052", + "auto_ref": true + }, + { + "doi": "10.1177/01622439251322530", + "apa": "Wang, J., Halffman, W., & Horbach, S. P. J. M. (2025). The Journal Attention Cycle: Indicators as Assets in the Chinese Scientific Publishing Economy. Science, Technology, & Human Values, 51(1), 218–245. https://doi.org/10.1177/01622439251322530", + "auto_ref": true + } + ] + }, + { + "name": "Publication, Peer Review, and Research Integrity", + "description": "This sub-cluster examines integrity issues in the dissemination phase of science – covering authorship ethics, peer review, and publication practices. It tackles questions like: Who deserves authorship and in what order? How to avoid ghost authorship (uncredited contributors) or gift/guest authorship (undeserved credit)? Students learn about authorship guidelines (e.g., International Committee of Medical Journal Editor ((ICMJE)) criteria) designed to ensure fair credit and accountability. We also discuss the role of peer review as a quality safeguard and the integrity challenges it faces – from biases in reviewer selection to cases of peer review fraud. The rise of predatory journals (which subvert quality standards for profit) is a contemporary integrity threat, potentially flooding literature with unvetted findings. Additionally, this sub-cluster emphasizes the importance of corrections and retractions as part of the self-correction mechanism of science. We explore whether increasing retraction rates signify improving vigilance or persistent problems​ (Bouter, 2024). Key themes include the responsibilities of journals (via ethics committees like the Committee on Publication Ethics ((COPE)) and editors in handling misconduct or honest errors, and emerging innovations like open peer review to improve transparency. By engaging with these topics, future researchers learn to navigate the publication process with integrity – ensuring proper attribution, objective review, and willingness to correct the record. Key Readings:", + "publications": [ + { + "doi": "10.1038/530027a", + "apa": "Allison, D. B., Brown, A. W., George, B. J., & Kaiser, K. A. (2016). Reproducibility: A tragedy of errors. Nature, 530(7588), 27–29. https://doi.org/10.1038/530027a", + "auto_ref": true + }, + { + "doi": "10.1016/j.techsoc.2025.102813", + "apa": "Andersen, J. P., Degn, L., Fishberg, R., Graversen, E. K., Horbach, S. P. J. M., Schmidt, E. K., Schneider, J. W., & Sørensen, M. P. (2025). Generative Artificial Intelligence (GenAI) in the research process – A survey of researchers’ practices and perceptions. Technology in Society, 81, 102813. https://doi.org/10.1016/j.techsoc.2025.102813", + "auto_ref": true + }, + { + "doi": "10.4037/ccn2019805", + "apa": "Bourgault, A. M. (2019). Predatory Conferences: Not the Meeting You Expected. Critical Care Nurse, 39(5), 10–12. https://doi.org/10.4037/ccn2019805", + "auto_ref": true + }, + { + "doi": "10.24318/cope.2019.1.4", + "apa": "Barbour, V., Kleinert, S., Wager, E., & Yentis, S. (2009). Guidelines for retracting articles. Committee on Publication Ethics. https://doi.org/10.24318/cope.2019.1.4", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-014-9521-4", + "apa": "Djuric, D. (2014). Penetrating the Omerta of Predatory Publishing: The Romanian Connection. Science and Engineering Ethics, 21(1), 183–202. https://doi.org/10.1007/s11948-014-9521-4", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pmed.1001563", + "apa": "Fanelli, D. (2013). Why Growing Retractions Are (Mostly) a Good Sign. PLoS Medicine, 10(12), e1001563. https://doi.org/10.1371/journal.pmed.1001563", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-019-03759-y", + "apa": "Grudniewicz, A., Moher, D., Cobey, K. D., Bryson, G. L., Cukier, S., Allen, K., Ardern, C., Balcom, L., Barros, T., Berger, M., Ciro, J. B., Cugusi, L., Donaldson, M. R., Egger, M., Graham, I. D., Hodgkinson, M., Khan, K. M., Mabizela, M., Manca, A., … Lalu, M. M. (2019). Predatory journals: no definition, no defence. Nature, 576(7786), 210–212. https://doi.org/10.1038/d41586-019-03759-y", + "auto_ref": true + }, + { + "doi": "10.4337/9781035300174.00015", + "apa": "Halffman, W., & Horbach, S. P. J. M. (2024). Designing journal peer review: diverse expectations, procedures and concerns. How to Edit and Manage a Successful Scholarly Journal, 68–78. https://doi.org/10.4337/9781035300174.00015", + "auto_ref": true + }, + { + "doi": "10.1111/bcp.15503", + "apa": "Haslberger, M., Schorr, S. G., Strech, D., & Haven, T. (2022). Preclinical efficacy in investigator’s brochures: Stakeholders’ views on measures to improve completeness and robustness. British Journal of Clinical Pharmacology, 89(1), 340–350. Portico. https://doi.org/10.1111/bcp.15503", + "auto_ref": true + }, + { + "doi": "10.1162/qss_a_00337", + "apa": "Hosseini, M., Horbach, S. P. J. M., Holmes, K., & Ross-Hellauer, T. (2025). Open Science at the generative AI turn: An exploratory analysis of challenges and opportunities. Quantitative Science Studies, 6, 22–45. https://doi.org/10.1162/qss_a_00337", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0186281", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2017). The ghosts of HeLa: How cell line misidentification contaminates the scientific literature. PLOS ONE, 12(10), e0186281. https://doi.org/10.1371/journal.pone.0186281", + "auto_ref": true + }, + { + "doi": "10.1186/s41073-018-0051-5", + "apa": "Horbach, S. P. J. M., & Halffman, W. ( W. (2018). The changing forms and expectations of peer review. Research Integrity and Peer Review, 3(1). https://doi.org/10.1186/s41073-018-0051-5", + "auto_ref": true + }, + { + "doi": "10.1007/s11192-018-2969-2", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2018). The ability of different peer review procedures to flag problematic publications. Scientometrics, 118(1), 339–373. https://doi.org/10.1007/s11192-018-2969-2", + "auto_ref": true + }, + { + "doi": "10.1007/s11024-019-09388-z", + "apa": "Horbach, S. P. J. M., & Halffman, W. (2019). Journal Peer Review and Editorial Evaluation: Cautious Innovator or Sleepy Giant? Minerva, 58(2), 139–161. https://doi.org/10.1007/s11024-019-09388-z", + "auto_ref": true + }, + { + "doi": "10.2340/17453674.2025.44353", + "apa": "Horbach, S. P. J. M., & Overgaard, S. (2025). Changing peer review practices: transforming roles and future challenges. Acta Orthopaedica, 96. https://doi.org/10.2340/17453674.2025.44353", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-020-01628-7", + "apa": "Horbach, S., Hepkema, W., & Halffman, W. (2020). Hundreds of journals’ editorial practices captured in database. Nature, 582(7810), 32–32. https://doi.org/10.1038/d41586-020-01628-7", + "auto_ref": true + }, + { + "doi": "10.1002/leap.1312", + "apa": "Horbach, S. P. J. M., Hepkema, W. M., & Halffman, W. (2020). The Platform for Responsible Editorial Policies: An initiative to foster editorial transparency in scholarly publishing. Learned Publishing, 33(3), 340–344. Portico. https://doi.org/10.1002/leap.1312", + "auto_ref": true + }, + { + "doi": "10.1162/qss_a_00076", + "apa": "Horbach, S. P. J. M. (2020). Pandemic publishing: Medical journals strongly speed up their publication process for COVID-19. Quantitative Science Studies, 1(3), 1056–1067. https://doi.org/10.1162/qss_a_00076", + "auto_ref": true + }, + { + "doi": "", + "apa": "Horbach, S. P. J. M. (2021). How the pandemic changed editorial peer review – and why we should wonder whether that’s desirable. Impact of Social Sciences (LSE). https://blogs.lse.ac.uk/impactofsocialsciences/2021/02/10/how-the-pandemic-changed-editorial-peer-review-and-why-we-should-wonder-whether-thats-desirable/", + "auto_ref": false + }, + { + "doi": "10.1093/reseval/rvaa037", + "apa": "Horbach, S. P. J. M. (2021). No time for that now! Qualitative changes in manuscript peer review during the Covid-19 pandemic. Research Evaluation, 30(3), 231–239. https://doi.org/10.1093/reseval/rvaa037", + "auto_ref": true + }, + { + "doi": "", + "apa": "Horbach, S. P. J. M., Ross-Hellauer, T., & Waltman, L. (2022). Sunlight not shadows: Double-anonymized peer review is not the progressive answer to status bias. OSF https://osf.io/preprints/osf/fqb5c_v1", + "auto_ref": false + }, + { + "doi": "", + "apa": "Horbach, S. P. J. M., Kalpazidou Schmidt, E., Fishberg, R., & Sørensen, M. P. (2024). Writing assistant, workhorse, or accelerator? How academics are using GenAI. Impact of Social Sciences (LSE). https://blogs.lse.ac.uk/impactofsocialsciences/2024/11/12/writing-assistant-workhorse-or-accelerator-how-academics-are-using-genai/", + "auto_ref": false + }, + { + "doi": "10.1186/s41073-023-00133-5", + "apa": "Hosseini, M., & Horbach, S. P. J. M. (2023). Fighting reviewer fatigue or amplifying bias? Considerations and recommendations for use of ChatGPT and other large language models in scholarly peer review. Research Integrity and Peer Review, 8(1). https://doi.org/10.1186/s41073-023-00133-5", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0023477", + "apa": "Marušić, A., Bošnjak, L., & Jerončić, A. (2011). A Systematic Review of Research on the Meaning, Ethics and Practices of Authorship across Scholarly Disciplines. PLoS ONE, 6(9), e23477. https://doi.org/10.1371/journal.pone.0023477", + "auto_ref": true + }, + { + "doi": "10.1038/s41598-024-54909-w", + "apa": "Meursinge Reynders, R. A., ter Riet, G., Di Girolamo, N., Cavagnetto, D., & Malički, M. (2024). Honorary authorship is highly prevalent in health sciences: systematic review and meta-analysis of surveys. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-54909-w", + "auto_ref": true + }, + { + "doi": "10.1186/s41256-023-00334-x", + "apa": "Nyangulu, W. J. (2023). Global health collaborative research: beyond mandatory collaboration to mandatory authorship. Global Health Research and Policy, 8(1). https://doi.org/10.1186/s41256-023-00334-x", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-022-02071-6", + "apa": "Oransky, I. (2022). Retractions are increasing, but not enough. Nature, 608(7921), 9–9. https://doi.org/10.1038/d41586-022-02071-6", + "auto_ref": true + }, + { + "doi": "10.1093/reseval/rvae004", + "apa": "Ross-Hellauer, T., & Horbach, S. P. J. M. (2024). Additional experiments required: A scoping review of recent evidence on key aspects of Open Peer Review. Research Evaluation, 33. https://doi.org/10.1093/reseval/rvae004", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pbio.3002255", + "apa": "Ross-Hellauer, T., Bouter, L. M., & Horbach, S. P. J. M. (2023). Open peer review urgently requires evidence: A call to action. PLOS Biology, 21(10), e3002255. https://doi.org/10.1371/journal.pbio.3002255", + "auto_ref": true + }, + { + "doi": "10.12688/f1000research.11369.2", + "apa": "Ross-Hellauer, T. (2017). What is open peer review? A systematic review. F1000Research, 6, 588. https://doi.org/10.12688/f1000research.11369.2", + "auto_ref": true + }, + { + "doi": "10.1258/jrsm.99.4.178", + "apa": "Smith, R. (2006). Peer Review: A Flawed Process at the Heart of Science and Journals. Journal of the Royal Society of Medicine, 99(4), 178–182. https://doi.org/10.1177/014107680609900414", + "auto_ref": true + }, + { + "doi": "", + "apa": "Sørensen, M. P., Horbach, S. P. J. M., Dorofeeva, O., & Schäfer Bak, M. (2024). Using generative artificial intelligence (GenAI) across different research phases: Cases, potential and risks [Report]. Danish Centre for Studies in Research and Research Policy (CFA), Aarhus University. https://tidsskrift.dk/cfasr/article/view/157222", + "auto_ref": false + }, + { + "doi": "10.1038/d41586-024-02358-w", + "apa": "Ro, C. (2024). What is it like to attend a predatory conference? Nature, 631(8022), 921–923. https://doi.org/10.1038/d41586-024-02358-w", + "auto_ref": true + } + ] + }, + { + "name": "Education and Training in Research Integrity", + "description": "Fostering a culture of integrity requires education. This sub-cluster looks at how researchers are taught (and learn) responsible conduct. Many jurisdictions and funders mandate Responsible Conduct of Research (RCR) training for students and staff – covering topics from data management and mentoring to publication ethics and conflicts of interest. We evaluate the impact of these educational programs: what works, what doesn’t, and how to innovate. Early meta-analyses showed that standard ethics training has modest positive effects on knowledge and attitudes​ (Antes et al., 2009)​, especially when using interactive, case-based approaches rather than dry lectures​ (Antes et al., 2009). Contemporary efforts aim to go beyond simply knowing the rules – to shape researchers’ ethical decision-making skills and “virtue ethics” (instilling values like honesty and care). We discuss novel training interventions, such as engaging researchers in moral case deliberation on real dilemmas or training faculty to model and transmit RI principles (e.g. “train-the-trainer” programs for PhD supervisors​ (Bouter, 2024). Policy initiatives like the Cape Town Statement (2022) emphasize that RI education should be continuous, assessed, and supported by institutions, not a one-off workshop. Overall, this sub-cluster reinforces that integrity is a skill set and mindset that can be nurtured. By empowering researchers through education, the community can proactively prevent misconduct and normalize ethical best practices as the default mode of work.", + "publications": [ + { + "doi": "10.1080/10508420903035380", + "apa": "Antes, A. L., Murphy, S. T., Waples, E. P., Mumford, M. D., Brown, R. P., Connelly, S., & Devenport, L. D. (2009). A Meta-Analysis of Ethics Instruction Effectiveness in the Sciences. Ethics & Behavior, 19(5), 379–402. https://doi.org/10.1080/10508420903035380", + "auto_ref": true + }, + { + "doi": "10.1017/cts.2024.10", + "apa": "Axfors, C., Malički, M., & Goodman, S. N. (2024). Research rigor and reproducibility in research education: A CTSA institutional survey. Journal of Clinical and Translational Science, 8(1). https://doi.org/10.1017/cts.2024.10", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2013.822248", + "apa": "DuBois, J. M., Anderson, E. E., Chibnall, J., Carroll, K., Gibb, T., Ogbuka, C., & Rubbelke, T. (2013). Understanding Research Misconduct: A Comparative Analysis of 120 Cases of Professional Wrongdoing. Accountability in Research, 20(5–6), 320–338. https://doi.org/10.1080/08989621.2013.822248", + "auto_ref": true + }, + { + "doi": "10.7554/eLife.83484", + "apa": "Haven, T. L., Abunijela, S., & Hildebrand, N. (2023). Biomedical supervisors’ role modeling of open science practices. ELife, 12. CLOCKSS. https://doi.org/10.7554/elife.83484", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2022.2071153", + "apa": "Haven, T., Bouter, L., Mennen, L., & Tijdink, J. (2022). Superb supervision: A pilot study on training supervisors to convey responsible research practices onto their PhD candidates. Accountability in Research, 30(8), 574–591. https://doi.org/10.1080/08989621.2022.2071153", + "auto_ref": true + }, + { + "doi": "10.3389/frma.2025.1670586", + "apa": "Haven, T., Plemmons, D., & Chau, D.-M. (2025). Editorial: Evaluating supervision and research leadership in promoting responsible research. Frontiers in Research Metrics and Analytics, 10. https://doi.org/10.3389/frma.2025.1670586", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2025.2457584", + "apa": "Haven, T. (2025). It takes two flints to start a fire: A focus group study into PhD supervision for responsible research. Accountability in Research, 32(5), 717–740. https://doi.org/10.1080/08989621.2025.2457584", + "auto_ref": true + }, + { + "doi": "10.1177/17470161231198402", + "apa": "Haven, T. L., Molewijk, B., Bouter, L., Widdershoven, G., Blom, F., & Tijdink, J. (2023). Can moral case deliberation in research groups help to navigate research integrity dilemmas? A pilot study. Research Ethics, 20(2), 219–238. https://doi.org/10.1177/17470161231198402", + "auto_ref": true + }, + { + "doi": "10.1080/23299460.2024.2414500", + "apa": "Horbach, S. P. J. M., Fishberg, R., Ulpts, S., & Degn, L. (2024). Thou Shalt Not! – How the institutional afterlife of research misconduct scandals shapes research integrity training. Journal of Responsible Innovation, 11(1). https://doi.org/10.1080/23299460.2024.2414500", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-023-00431-7", + "apa": "Inguaggiato, G., Labib, K., Evans, N., Blom, F., Bouter, L., & Widdershoven, G. (2023). The Contribution of Moral Case Deliberation to Teaching RCR to PhD Students. Science and Engineering Ethics, 29(2). https://doi.org/10.1007/s11948-023-00431-7", + "auto_ref": true + }, + { + "doi": "", + "apa": "Kalichman, M. (2013). A brief history of RCR education. Accountability in research, 20(5-6), 380-394. doi.org/10.1080/08989621.2013.822260 – Traces the development of research ethics education from the 1980s to present. Reviews U.S. and international efforts to require training and the evolution of content, highlighting persistent challenges in assessing effectiveness and engagement.", + "auto_ref": false + }, + { + "doi": "10.1007/s10648-021-09630-9", + "apa": "Katsarov, J., Andorno, R., Krom, A., & van den Hoven, M. (2021). Effective Strategies for Research Integrity Training—a Meta-analysis. Educational Psychology Review, 34(2), 935–955. https://doi.org/10.1007/s10648-021-09630-9", + "auto_ref": true + }, + { + "doi": "10.7554/eLife.89736", + "apa": "Kohrs, F. E., Auer, S., Bannach-Brown, A., Fiedler, S., Haven, T. L., Heise, V., Holman, C., Azevedo, F., Bernard, R., Bleier, A., Bössel, N., Cahill, B. P., Castro, L. J., Ehrenhofer, A., Eichel, K., Frank, M., Frick, C., Friese, M., Gärtner, A., … Weissgerber, T. L. (2023). Eleven strategies for making reproducible research and open science training the norm at research institutions. ELife, 12. CLOCKSS. https://doi.org/10.7554/elife.89736", + "auto_ref": true + }, + { + "doi": "10.1007/s43683-023-00131-5", + "apa": "Kreeger, P. K. (2024). Rethinking the Responsible Conduct of Research (RCR) Course. Biomedical Engineering Education, 4(2), 251–257. https://doi.org/10.1007/s43683-023-00131-5", + "auto_ref": true + }, + { + "doi": "10.3389/frma.2025.1531467", + "apa": "Lacey, S., Haven, T., Santos, R., Farrelly, T., Murray, M., & Kavouras, P. (2025). A roadmap to good practice for training supervisors and leadership: a European perspective. Frontiers in Research Metrics and Analytics, 10. https://doi.org/10.3389/frma.2025.1531467", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2022.2154154", + "apa": "Labib, K., Pizzolato, D., Stappers, P. J., Evans, N., Lechner, I., Widdershoven, G., Bouter, L., Dierickx, K., Bergema, K., & Tijdink, J. (2023). Using co-creation methods for research integrity guideline development – how, what, why and when? Accountability in Research, 31(6), 531–556. https://doi.org/10.1080/08989621.2022.2154154", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-021-00322-9", + "apa": "Labib, K., Roje, R., Bouter, L., Widdershoven, G., Evans, N., Marušić, A., Mokkink, L., & Tijdink, J. (2021). Important Topics for Fostering Research Integrity by Research Performing and Research Funding Organizations: A Delphi Consensus Study. Science and Engineering Ethics, 27(4). https://doi.org/10.1007/s11948-021-00322-9", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-023-00444-2", + "apa": "Labib, K., Evans, N., Pizzolato, D., Aubert Bonn, N., Widdershoven, G., Bouter, L., Konach, T., Langendam, M., Dierickx, K., & Tijdink, J. (2023). Co-creating Research Integrity Education Guidelines for Research Institutions. Science and Engineering Ethics, 29(4). https://doi.org/10.1007/s11948-023-00444-2", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-020-02847-8", + "apa": "Mejlgaard, N., Bouter, L. M., Gaskell, G., Kavouras, P., Allum, N., Bendtsen, A.-K., Charitidis, C. A., Claesen, N., Dierickx, K., Domaradzka, A., Reyes Elizondo, A., Foeger, N., Hiney, M., Kaltenbrunner, W., Labib, K., Marušić, A., Sørensen, M. P., Ravn, T., Ščepanović, R., … Veltri, G. A. (2020). Research integrity: nine ways to move from talk to walk. Nature, 586(7829), 358–360. https://doi.org/10.1038/d41586-020-02847-8", + "auto_ref": true + }, + { + "doi": "10.1186/s12910-021-00637-z", + "apa": "Pizzolato, D., & Dierickx, K. (2021). Stakeholders’ perspectives on research integrity training practices: a qualitative study. BMC Medical Ethics, 22(1). https://doi.org/10.1186/s12910-021-00637-z", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2022.2112033", + "apa": "Pizzolato, D., Labib, K., Skoulikaris, N., Evans, N., Roje, R., Kavouras, P., Aubert Bonn, N., Dierickx, K., & Tijdink, J. (2022). How can research institutions support responsible supervision and leadership? Accountability in Research, 31(3), 173–195. https://doi.org/10.1080/08989621.2022.2112033", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2023.2239145", + "apa": "Rasmussen, L. M. (2023). Why and how to incorporate issues of race/ethnicity and gender in research integrity education. Accountability in Research, 31(7), 944–967. https://doi.org/10.1080/08989621.2023.2239145", + "auto_ref": true + }, + { + "doi": "10.1007/s40979-025-00186-7", + "apa": "Salwén, H., Holm, C., Achermann, G., Asaduzzaman, M., Blom, F., Dwojak-Matras, A., Groenink, L., Gruber, B., van den Hoven, M., Ristic, D. I., Iphofen, R., & Priess-Buchheit, J. (2025). Teaching research integrity: a manual of good practices: an outline. International Journal for Educational Integrity, 21(1). https://doi.org/10.1007/s40979-025-00186-7", + "auto_ref": true + }, + { + "doi": "10.1126/science.1236373", + "apa": "Steneck, N. H. (2013). Global Research Integrity Training. Science, 340(6132), 552–553. https://doi.org/10.1126/science.1236373", + "auto_ref": true + }, + { + "doi": "10.1007/s11948-022-00425-x", + "apa": "van den Hoven, M., Lindemann, T., Zollitsch, L., & Prieß-Buchheit, J. (2023). A Taxonomy for Research Integrity Training: Design, Conduct, and Improvements in Research Integrity Courses. Science and Engineering Ethics, 29(3). https://doi.org/10.1007/s11948-022-00425-x", + "auto_ref": true + }, + { + "doi": "10.1007/s40979-023-00139-y", + "apa": "Hoven, M. vd, Mol, H., & Verhoeff, R. (2023). Evaluating empowerment towards responsible conduct of research in a small private online course. International Journal for Educational Integrity, 19(1). https://doi.org/10.1007/s40979-023-00139-y", + "auto_ref": true + }, + { + "doi": "", + "apa": "van den Hoven, M., & van Loon, M. (2025). Responsible conduct of research [Online course]. Utrecht University. https://www.coursera.org/learn/research-integrity", + "auto_ref": false + }, + { + "doi": "", + "apa": "Watts, Logan & Medeiros, Kelsey & Mulhearn, Tyler & Steele, Logan & Connelly, Shane & Mumford, Michael. (2017). Are Ethics Training Programs Improving? A Meta-Analytic Review of Past and Present Ethics Instruction in the Sciences. Ethics & Behavior. 27. 351-384. 10.1080/10508422.2016.1182025.", + "auto_ref": false + } + ] + }, + { + "name": "Research Integrity, Social Responsibility, and Equity", + "description": "This sub-cluster broadens the scope of research integrity to include the social and justice dimensions of research practice. It asks: What obligations do researchers have to society and to the communities affected by their work? Traditional RI focuses on truthfulness and accuracy, but integrity also entails conducting research responsibly with regard to its societal impact. Topics here include inclusive citation and recognition practices (avoiding exclusion or bias in credit), ensuring research agendas are not harmful or exploitative, and global equity in collaborations. For example, the Montreal Statement (2013) provides guidance for equitable partnerships, stressing respect, clarity, and fairness when researchers from high-income and low-income settings collaborate. We also explore contemporary issues like “ethics dumping” – exporting unethical research to regions with lax oversight – and the global efforts to counter it with codes of conduct​ (Zhaksylyk et al., 2023). Open Science intersects with equity by pushing for accessibility of knowledge and participation from diverse stakeholders (e.g. citizen science, indigenous knowledge considerations). Readings encourage reflection on how striving for integrity means striving for a research enterprise that is not only reliable but also just. This includes acknowledging and addressing structural biases (racism, sexism, colonialism) in research contexts – because an equitable, inclusive research culture is integral to truly responsible science.", + "publications": [ + { + "doi": "", + "apa": "ALL European Academies (ALLEA). (2021). Truth, Trust and Expertise – The Ethics of Science and Public Engagement. Report found at the bottom of page alongside six other reports – A report examining the relationship between scientific integrity and public trust. It covers ethical science communication, avoiding hype, and the duty of researchers to engage honestly with society. Highlights that maintaining public trust is an aspect of research integrity, requiring transparency and humility on the part of experts.", + "auto_ref": false + }, + { + "doi": "10.1371/journal.pmed.1001089", + "apa": "Boga, M., Davies, A., Kamuya, D., Kinyanjui, S. M., Kivaya, E., Kombe, F., Lang, T., Marsh, V., Mbete, B., Mlamba, A., Molyneux, S., Mulupi, S., & Mwalukore, S. (2011). Strengthening the Informed Consent Process in International Health Research through Community Engagement: The KEMRI-Wellcome Trust Research Programme Experience. PLoS Medicine, 8(9), e1001089. https://doi.org/10.1371/journal.pmed.1001089", + "auto_ref": true + }, + { + "doi": "", + "apa": "Chatfield, Kate & Schroeder, Doris & Singh, Michelle & Chennells, Roger & herissone-kelly, peter. (2019). Equitable Research Partnerships A Global Code of Conduct to Counter Ethics Dumping. 32–34. ISBN: 978-3-030-15745-6 – Presents a Global Code of Conduct aimed at preventing researchers from exploiting vulnerable populations or regions with weaker oversight. Offers four pillars (fairness, respect, care, honesty) to guide projects in low-resource settings, aligning integrity with social justice.", + "auto_ref": false + }, + { + "doi": "10.31219/osf.io/bf286", + "apa": "Horn, L., Alba, S., Blom, F., Faure, M., Flack-Davison, E., Gopalakrishna, G., IJsselmuiden, C., Labib, K., Lavery, J. V., Masekela, R., Schroeder, D., Simon, N., Van Zyl, C., Vasconcelos, S., Visagie, R., & Kombe, F. (2022). Fostering Research Integrity through the promotion of fairness, equity and diversity in research collaborations and contexts: Towards a Cape Town Statement (pre-conference discussion paper). https://doi.org/10.31219/osf.io/bf286", + "auto_ref": true + }, + { + "doi": "10.1038/d41586-023-00855-y", + "apa": "Horn, L., Alba, S., Gopalakrishna, G., Kleinert, S., Kombe, F., Lavery, J. V., & Visagie, R. G. (2023). The Cape Town Statement on fairness, equity and diversity in research. Nature, 615(7954), 790–793. https://doi.org/10.1038/d41586-023-00855-y", + "auto_ref": true + }, + { + "doi": "10.1177/1556264615592385", + "apa": "Jao, I., Kombe, F., Mwalukore, S., Bull, S., Parker, M., Kamuya, D., Molyneux, S., & Marsh, V. (2015). Involving Research Stakeholders in Developing Policy on Sharing Public Health Research Data in Kenya. Journal of Empirical Research on Human Research Ethics, 10(3), 264–277. https://doi.org/10.1177/1556264615592385", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pone.0135545", + "apa": "Jao, I., Kombe, F., Mwalukore, S., Bull, S., Parker, M., Kamuya, D., Molyneux, S., & Marsh, V. (2015). Research Stakeholders’ Views on Benefits and Challenges for Public Health Research Data Sharing in Kenya: The Importance of Trust and Social Relations. PLOS ONE, 10(9), e0135545. https://doi.org/10.1371/journal.pone.0135545", + "auto_ref": true + }, + { + "doi": "10.1111/dewb.12014", + "apa": "Kamuya, D. M., Marsh, V., Kombe, F. K., Geissler, P. W., & Molyneux, S. C. (2013). Engaging Communities to Strengthen Research Ethics in Low‐Income Settings: Selection and Perceptions of Members of a Network of Representatives in Coastal Kenya. Developing World Bioethics, 13(1), 10–20. Portico. https://doi.org/10.1111/dewb.12014", + "auto_ref": true + }, + { + "doi": "10.1177/20966083251329632", + "apa": "Knibbe, M., de Rijcke, S., & Penders, B. (2025). Care for the soul of science: Equity and virtue in reform and reformation. Cultures of Science, 8(1), 12–23. https://doi.org/10.1177/20966083251329632", + "auto_ref": true + }, + { + "doi": "10.1093/acprof:oso/9780199732623.001.0001", + "apa": "Kourany, J. A. (2010). Philosophy of Science after Feminism. https://doi.org/10.1093/acprof:oso/9780199732623.001.0001", + "auto_ref": true + }, + { + "doi": "10.1371/journal.pbio.3001036", + "apa": "Labib, K., & Evans, N. (2021). Gender, diversity, and the responsible assessment of researchers. PLOS Biology, 19(4), e3001036. https://doi.org/10.1371/journal.pbio.3001036", + "auto_ref": true + }, + { + "doi": "10.31222/osf.io/zr35u_v1", + "apa": "Crespo López, M. de los Á., Pallise Perello, C., de Ridder, J., & Labib, K. (2025). Open Science as Confused: Contradictory and Conflicting Discourses in Open Science Guidance to Researchers. https://doi.org/10.31222/osf.io/zr35u_v1", + "auto_ref": true + }, + { + "doi": "10.7202/1118901ar", + "apa": "Labib, K. (2025). Research Integrity and Research Fairness: Harmonious or in Conflict? Canadian Journal of Bioethics, 8(3), 44–54. https://doi.org/10.7202/1118901ar", + "auto_ref": true + }, + { + "doi": "10.1186/1472-6939-14-41", + "apa": "Marsh, V., Kombe, F., Fitzpatrick, R., Williams, T. N., Parker, M., & Molyneux, S. (2013). Consulting communities on feedback of genetic findings in international health research: sharing sickle cell disease and carrier information in coastal Kenya. BMC Medical Ethics, 14(1). https://doi.org/10.1186/1472-6939-14-41", + "auto_ref": true + }, + { + "doi": "", + "apa": "Montreal Statement on Research Integrity in Cross-Boundary Research Collaborations (2013). – Articulates 20 principles to ensure ethical and equitable conduct in international collaborations (e.g. fair division of labor and credit, respect for local norms, benefit-sharing, transparency between partners). Emphasizes that integrity requires fairness when research transcends borders and cultures.", + "auto_ref": false + }, + { + "doi": "10.1371/journal.pone.0113112", + "apa": "Njue, M., Kombe, F., Mwalukore, S., Molyneux, S., & Marsh, V. (2014). What Are Fair Study Benefits in International Health Research? Consulting Community Members in Kenya. PLoS ONE, 9(12), e113112. https://doi.org/10.1371/journal.pone.0113112", + "auto_ref": true + }, + { + "doi": "10.1186/s41256-023-00334-x", + "apa": "Nyangulu, W. J. (2023). Global health collaborative research: beyond mandatory collaboration to mandatory authorship. Global Health Research and Policy, 8(1). https://doi.org/10.1186/s41256-023-00334-x", + "auto_ref": true + }, + { + "doi": "10.1080/08989621.2023.2239145", + "apa": "Rasmussen, L. M. (2023). Why and how to incorporate issues of race/ethnicity and gender in research integrity education. Accountability in Research, 31(7), 944–967. https://doi.org/10.1080/08989621.2023.2239145", + "auto_ref": true + }, + { + "doi": "", + "apa": "Shamoo, A. E., & Resnik, D. B. (2009). Responsible conduct of research. Oxford University Press. – Discusses challenges of maintaining RI in a global context: varying cultural norms, differing regulations, and issues like intellectual property, benefit sharing, and authorship across borders. Affirms that core RI principles are universal and must underpin international scientific collaborations and technology transfer.", + "auto_ref": false + } + ] + } + ] + } + ] +} \ No newline at end of file diff --git a/layouts/shortcodes/clusters_display.html b/layouts/shortcodes/clusters_display.html new file mode 100644 index 00000000000..98cc5f80ad6 --- /dev/null +++ b/layouts/shortcodes/clusters_display.html @@ -0,0 +1,367 @@ +{{/* clusters_display.html - Renders all FORRT clusters from data/clusters_v4.json */}} +{{ $data := site.Data.clusters_v4 }} +{{ if not $data }} +

Error: clusters_v4.json data not found. Run python3 scripts/parse_clusters_to_sheet.py --export-json.

+ {{ return }} +{{ end }} + +{{ $colors := slice "#cacfdc" "#eadce6" "#d4e4d9" "#BDC5CA" "#dce4ea" "#e8ddd4" "#c9dbcb" "#d9cfe0" "#cddde3" "#e0d8cc" "#d4dce8" }} +{{ $arrowColors := slice "#6070a0" "#a05080" "#408060" "#607080" "#5080a0" "#a08060" "#509060" "#8060a0" "#5090a0" "#907050" "#6070a0" }} + +
+ + {{/* ===== SEARCH BAR (above sidebar+content) ===== */}} +
+ + +
+ + {{/* ===== MOBILE NAV TOGGLE ===== */}} + + +
+ {{/* ===== SIDEBAR ===== */}} +
+
+
Clusters & Sub-clusters
+ +
+
+ + {{/* ===== MAIN CONTENT ===== */}} +
+ {{ range $ci, $cluster := $data.clusters }} + {{ $cid := printf "cluster-%d" (int $cluster.number) }} + {{ $color := index $colors (mod $ci (len $colors)) }} + {{ $totalPubs := 0 }}{{ range $cluster.sub_clusters }}{{ $totalPubs = add $totalPubs (len .publications) }}{{ end }} + +
+
+

+ {{ (int $cluster.number) }} + {{ $cluster.name }} +

+ {{ len $cluster.sub_clusters }} sub-clusters · {{ $totalPubs }} references +
+ + {{ if $cluster.description }} +

{{ $cluster.description }}

+ {{ end }} + + {{/* Sub-cluster tabs */}} + {{ if gt (len $cluster.sub_clusters) 0 }} + + +
+ {{ range $si, $sc := $cluster.sub_clusters }} + {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} +
+ +

{{ $sc.name }}

+ + {{ if $sc.description }} +

{{ $sc.description }}

+ {{ end }} + + {{ if $sc.publications }} +
    + {{ range $sc.publications }} +
  • + {{ $ref := .apa }} + {{/* Strip DOI URL from text - we show it separately */}} + {{ $ref = replaceRE `\s*https?://(?:dx\.)?doi\.org/\S+` "" $ref }} + {{ $ref = replaceRE `\s+$` "" $ref }} + {{/* Strip dangerous tags but keep i/em for italics (data from doi.org is trusted) */}} + {{ $ref = replaceRE `]*>.*?` "" $ref }} + {{ $ref = replaceRE `]*>.*?` "" $ref }} + {{/* Linkify remaining URLs */}} + {{ $ref = replaceRE `(https?://\S+)` `$1` $ref }} + {{ $ref | safeHTML }} + {{ if .doi }} + {{ $doiURL := printf "https://doi.org/%s" .doi }} + {{ $doiURL }} + {{ end }} +
    • + {{ end }} +
+ {{ else }} +

No publications listed for this sub-cluster yet.

+ {{ end }} + +
+ {{ end }} +
+ {{ end }} +
+ + {{ end }} +
+
+
+ +{{/* ===== JAVASCRIPT ===== */}} + diff --git a/scripts/parse_clusters_to_sheet.py b/scripts/parse_clusters_to_sheet.py new file mode 100644 index 00000000000..bf375991560 --- /dev/null +++ b/scripts/parse_clusters_to_sheet.py @@ -0,0 +1,1126 @@ +#!/usr/bin/env python3 +"""Parse FORRT Clusters v4.1 Google Doc and populate a Google Sheet. + +Usage: + python parse_clusters_to_sheet.py # Full run + python parse_clusters_to_sheet.py --dry-run # Parse only, print stats + python parse_clusters_to_sheet.py --skip-doi # Skip DOI lookups +""" + +import argparse +import json +import os +import re +import subprocess +import sys +import time +import urllib.request +from dataclasses import dataclass, field + +# --- Constants --- +DOC_URL = "https://docs.google.com/document/d/1_TRh7z3Bv_tdxGqjdWMm4kfQerTYvYw3e4wvQLNpTDQ/export?format=txt" +SHEET_ID = "1BxYioDDE2GftOFdQGtH0lVguEUWNQ_k8Ls-bdRn8RRo" +SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__)) +DEFAULT_CACHE = os.path.join(SCRIPT_DIR, "doi_cache.json") + +# --- Regex --- +ANNOTATION_RE = re.compile(r'\[([a-z]{1,3})\]') +CLUSTER_RE = re.compile(r'^Cluster\s+(\d+)\s*:\s*(.+)') +BULLET_RE = re.compile(r'^\s*\*\s+') +DOI_RE = re.compile(r'https?://(?:dx\.)?doi\.org/(\S+)') +PROXY_DOI_RE = re.compile(r'https?://\S*doi-org\S+?/') +C11_SC_RE = re.compile(r'^Sub-cluster\s+(\d+)\s*:\s*(.+)', re.IGNORECASE) +SEPARATOR_RE = re.compile(r'^_{5,}$') + + +# --- Data classes --- +@dataclass +class Cluster: + number: int + name: str + description: str + annotations: str + sub_clusters: list = field(default_factory=list) + + +@dataclass +class SubCluster: + name: str + cluster_name: str + description: str + annotations: str + raw_citations: list = field(default_factory=list) + + +@dataclass +class Publication: + sub_cluster: str + doi: str + apa_reference: str + bibtex: str + auto_ref: bool + annotations: str + + +# --- Helpers --- +def extract_annotations(text): + """Extract annotation markers like [a], [ab] and return (cleaned_text, annot_string).""" + found = ANNOTATION_RE.findall(text) + cleaned = ANNOTATION_RE.sub('', text) + return cleaned, ', '.join(found) if found else '' + + +def normalize_name(s): + """Normalize for comparison: lowercase, collapse whitespace, strip punctuation.""" + s = s.lower().strip() + # Replace slashes and ampersands with spaces to separate words + # e.g., "community/citizen" -> "community citizen", "Sexuality & Gender" -> "sexuality gender" + s = s.replace('/', ' ').replace('&', ' ') + s = re.sub(r'\s+', ' ', s) + s = s.rstrip('.,:;') + return s + + +def extract_doi(text): + """Extract DOI string from citation text, or None.""" + m = DOI_RE.search(text) + if not m: + return None + doi = m.group(1) + # Strip trailing punctuation that's not part of the DOI + doi = doi.rstrip('.,;:)> ') + # Remove trailing period if present (common in sentence-ending DOIs) + if doi.endswith('.'): + doi = doi[:-1] + return doi + + +def clean_citation_text(raw): + """Clean a raw citation: strip annotations, normalize whitespace.""" + text, annots = extract_annotations(raw) + # Collapse internal whitespace + text = re.sub(r'\s+', ' ', text).strip() + return text, annots + + +# --- Document fetching --- +def fetch_document(): + """Download Google Doc as plain text.""" + print("Fetching document...") + req = urllib.request.Request(DOC_URL) + with urllib.request.urlopen(req) as resp: + text = resp.read().decode('utf-8-sig') + lines = text.splitlines() + print(f" {len(lines)} lines downloaded") + return lines + + +def preprocess_lines(lines): + """Normalize proxy DOIs and strip trailing whitespace.""" + result = [] + for line in lines: + line = PROXY_DOI_RE.sub('https://doi.org/', line) + result.append(line.rstrip()) + return result + + +# --- Document parsing --- +def find_content_start(lines): + """Find line index where cluster content begins (Cluster 1 followed by Description).""" + for i, line in enumerate(lines): + clean, _ = extract_annotations(line.strip()) + m = CLUSTER_RE.match(clean.strip()) + if m and m.group(1) == '1': + # Check next few lines for "Description" + for j in range(i + 1, min(i + 5, len(lines))): + if lines[j].strip() == 'Description': + return i + raise ValueError("Could not find content start (Cluster 1 with Description)") + + +def find_cluster_boundaries(lines, content_start): + """Return [(line_idx, cluster_num, clean_name, annotations)] for all 11 clusters.""" + boundaries = [] + seen = set() + + for i in range(content_start, len(lines)): + clean, annots = extract_annotations(lines[i].strip()) + m = CLUSTER_RE.match(clean.strip()) + if m: + num = int(m.group(1)) + if num in seen: + break # Hit the footer ToC + seen.add(num) + name = re.sub(r'\s+', ' ', m.group(2)).strip() + boundaries.append((i, num, name, annots)) + if num == 11: + break + return boundaries + + +def find_content_end(lines, cluster_11_start): + """Find end of Cluster 11 content (before footer ToC).""" + for i in range(cluster_11_start + 1, len(lines)): + clean, _ = extract_annotations(lines[i].strip()) + m = CLUSTER_RE.match(clean.strip()) + if m: + return i + return len(lines) + + +def parse_cluster_toc(lines, desc_start, section_end): + """Parse cluster description and extract sub-cluster ToC names. + + Returns (description_text, [toc_names]). + """ + description_parts = [] + toc_names = [] + in_toc = False + + i = desc_start + while i < section_end: + stripped = lines[i].strip() + + if not stripped: + if in_toc: + break # Blank line after ToC bullets = end of description area + i += 1 + continue + + if BULLET_RE.match(stripped): + in_toc = True + name_raw = BULLET_RE.sub('', stripped) + name_clean, _ = extract_annotations(name_raw) + name_clean = re.sub(r'\s+', ' ', name_clean).strip() + if name_clean: + toc_names.append(name_clean) + else: + if in_toc: + # Non-bullet after bullets - might be continuation or end + # Check if it looks like a sub-cluster heading (not indented) + if not lines[i].startswith(' '): + break + # Otherwise it's a continuation of a ToC name + if toc_names: + toc_names[-1] += ' ' + stripped + else: + description_parts.append(stripped) + + i += 1 + + description = ' '.join(description_parts) + return description, toc_names, i + + +YEAR_IN_PARENS_RE = re.compile(r'\(\d{4}') +ND_RE = re.compile(r'\(n\.d\.\)') + + +def looks_like_citation(text): + """Check if text looks like a citation rather than a heading.""" + if YEAR_IN_PARENS_RE.search(text): + return True + if ND_RE.search(text): + return True + if 'doi.org/' in text.lower(): + return True + if 'https://' in text or 'http://' in text: + return True + return False + + +STOP_WORDS = frozenset( + 'the a an and or in on of to for is are was were be been its it we they ' + 'that this with by as at from not but how when why what which their have ' + 'has had can will do does did about than more also'.split() +) + + +def is_toc_match(line_text, toc_lookup): + """Check if line_text matches a known ToC name. Returns matched name or None.""" + norm = normalize_name(line_text) + if norm in toc_lookup: + return toc_lookup[norm] + + # Only fuzzy-match short text (long text = description paragraph, not heading) + words = norm.split() + if len(words) > 20: + return None + + # Word overlap excluding stop words + line_words = set(words) - STOP_WORDS + if len(line_words) < 1: # Need at least one meaningful word + return None + + for toc_norm, toc_name in toc_lookup.items(): + toc_words = set(toc_norm.split()) - STOP_WORDS + if len(toc_words) < 1: + continue + + overlap = len(line_words & toc_words) + + # Special case: single-word ToC items + # Only match if: (1) line has few words, and (2) the single ToC word is present + if len(toc_words) == 1 and overlap == 1 and len(line_words) <= 3: + return line_text # Use content heading text + + # Multi-word matching: need sufficient overlap + denom = min(len(line_words), len(toc_words)) + if denom > 1 and overlap / denom >= 0.6: + return line_text # Use content heading text + return None + + +def parse_subclusters_standard(lines, start, end, toc_names, cluster_name): + """Parse sub-cluster sections for Clusters 1-10. + + Heading detection combines ToC matching with structural/heuristic detection: + 1. Lines matching ToC names are always headings + 2. Non-citation lines that are short and don't look like citations are headings + 3. Lines that look like citations are treated as citation text + """ + toc_lookup = {normalize_name(n): n for n in toc_names} + + sub_clusters = [] + current_sc = None + current_desc = [] + current_cites = [] + + # States: 'await_heading', 'in_description', 'in_citations' + state = 'await_heading' + + def save_current(): + nonlocal current_sc + if current_sc: + current_sc.description = ' '.join(current_desc) + current_sc.raw_citations = list(current_cites) + sub_clusters.append(current_sc) + + i = start + while i < end: + raw_line = lines[i] + stripped = raw_line.strip() + + # Blank lines + if not stripped: + if state in ('in_citations', 'in_description'): + state = 'await_heading' + i += 1 + continue + + # Separators + if SEPARATOR_RE.match(stripped): + if state in ('in_citations', 'in_description'): + state = 'await_heading' + i += 1 + continue + + # FILTER: Skip orphaned periods and other junk at column 0 + if stripped == '.' or (stripped and len(stripped) <= 1 and not BULLET_RE.match(stripped)): + i += 1 + continue + + has_bullet = bool(BULLET_RE.match(stripped)) + + # Bullet lines + if has_bullet: + bullet_text = BULLET_RE.sub('', stripped) + clean_bullet, bullet_annots = extract_annotations(bullet_text) + clean_bullet = re.sub(r'\s+', ' ', clean_bullet).strip() + + # Check for bullet-prefixed heading (rare but happens) + # Only accept as heading if: matches ToC AND not a citation-like fragment + toc_match = is_toc_match(clean_bullet, toc_lookup) + + # Filter: reject incomplete citations (name + title but no year/DOI/URL) + is_incomplete_citation = ( + ': ' in clean_bullet and + not looks_like_citation(clean_bullet) and + 'doi.org' not in clean_bullet.lower() and + 'https://' not in clean_bullet.lower() and + any(surname in clean_bullet for surname in ['Suber', 'Peter', 'Methods']) and + '(' not in clean_bullet # No year in parens + ) + + if toc_match and not looks_like_citation(clean_bullet) and not is_incomplete_citation: + save_current() + current_sc = SubCluster( + name=clean_bullet, cluster_name=cluster_name, + description='', annotations=bullet_annots, + ) + current_desc = [] + current_cites = [] + state = 'in_description' + i += 1 + continue + + # Regular citation bullet + if current_sc is not None: + current_cites.append(bullet_text) + state = 'in_citations' + i += 1 + continue + + # Non-bullet line: heading, description, or citation continuation? + clean_text, line_annots = extract_annotations(stripped) + clean_text = re.sub(r'\s+', ' ', clean_text).strip() + is_indented = raw_line.startswith(' ') # 8+ spaces + + # 1. Indented lines are always continuations (never headings) + if is_indented: + if current_cites: + current_cites[-1] += ' ' + stripped + elif current_sc is not None: + current_desc.append(stripped) + i += 1 + continue + + # 2. Check ToC match (strongest heading signal, non-indented only) + toc_match = is_toc_match(clean_text, toc_lookup) + if toc_match and not looks_like_citation(clean_text): + save_current() + current_sc = SubCluster( + name=clean_text, cluster_name=cluster_name, + description='', annotations=line_annots, + ) + current_desc = [] + current_cites = [] + state = 'in_description' + i += 1 + continue + + # 3. If it looks like a citation, treat as citation/continuation + if looks_like_citation(clean_text): + if current_cites: + current_cites[-1] += ' ' + stripped + elif current_sc is not None: + current_cites.append(stripped) + state = 'in_citations' + i += 1 + continue + + # 4. Structural heading: non-indented, non-citation, after blank lines only + # FILTER: Reject placeholder text and incomplete citations + is_placeholder = clean_text in ('INSERT DESCRIPTION', 'Description') + + is_orphaned_citation = ( + not looks_like_citation(clean_text) and + ': ' in clean_text and + 'doi.org' not in clean_text.lower() and + len(clean_text) < 150 and + len(clean_text.split()) > 5 and + any(word.lower() in clean_text.lower() for word in ['suber', 'peter', 'methods', 'rights']) + ) + + if state == 'await_heading' and len(clean_text) < 300 and not is_placeholder and not is_orphaned_citation: + save_current() + current_sc = SubCluster( + name=clean_text, cluster_name=cluster_name, + description='', annotations=line_annots, + ) + current_desc = [] + current_cites = [] + state = 'in_description' + i += 1 + continue + + # 5. Description text (after heading, before citations) + if state == 'in_description': + current_desc.append(stripped) + i += 1 + continue + + # Default: append to current citations as continuation + if current_sc and current_cites: + current_cites[-1] += ' ' + stripped + i += 1 + + save_current() + return sub_clusters + + +def parse_cluster_11(lines, start, end): + """Parse Cluster 11 which has different formatting.""" + # Extract description: text after "Cluster Description" until the internal ToC + desc_parts = [] + i = start + 1 # skip the "Cluster 11: ..." heading + found_desc = False + + # Find description paragraph + while i < end: + stripped = lines[i].strip() + if stripped in ('Cluster Description', 'Research Integrity Cluster'): + found_desc = True + i += 1 + continue + if found_desc and stripped: + # Check if we've hit the internal ToC + if C11_SC_RE.match(extract_annotations(stripped)[0].strip()): + break + if stripped in ('Cross-Cluster Integration and Synergies', + 'Possible Additional Sub-clusters?'): + break + desc_parts.append(stripped) + elif found_desc and not stripped and desc_parts: + # Blank line after description content + # Check if next non-blank line is a sub-cluster or ToC + for j in range(i + 1, min(i + 5, end)): + next_s = lines[j].strip() + if next_s: + next_clean, _ = extract_annotations(next_s) + if (C11_SC_RE.match(next_clean.strip()) or + next_s == 'Research Integrity (RI) Cluster'): + found_desc = False # Stop collecting description + break + if not found_desc: + break + i += 1 + + description = ' '.join(desc_parts) + + # Find where sub-cluster content begins (after separator) + sc_content_start = None + for j in range(i, end): + if SEPARATOR_RE.match(lines[j].strip()): + sc_content_start = j + 1 + break + + if sc_content_start is None: + sc_content_start = i + + # Parse sub-clusters + sub_clusters = [] + current_sc = None + current_desc = [] + current_cites = [] + in_key_readings = False + + def save_current(): + nonlocal current_sc + if current_sc: + current_sc.description = ' '.join(current_desc) + current_sc.raw_citations = list(current_cites) + sub_clusters.append(current_sc) + + j = sc_content_start + while j < end: + stripped = lines[j].strip() + + if not stripped: + j += 1 + continue + + # Stop at editorial separator + if SEPARATOR_RE.match(stripped): + # Check if next non-blank line is a Sub-cluster heading + is_next_sc = False + for k in range(j + 1, min(j + 5, end)): + next_s = lines[k].strip() + if next_s: + next_clean, _ = extract_annotations(next_s) + if C11_SC_RE.match(next_clean.strip()): + is_next_sc = True + break + if not is_next_sc: + break # Editorial section, stop parsing + j += 1 + continue + + clean_stripped, line_annots = extract_annotations(stripped) + clean_stripped = clean_stripped.strip() + + # Check for sub-cluster heading + m = C11_SC_RE.match(clean_stripped) + if m: + save_current() + sc_name = re.sub(r'\s+', ' ', m.group(2)).strip() + current_sc = SubCluster( + name=sc_name, cluster_name='Research Integrity', + description='', annotations=line_annots, raw_citations=[] + ) + current_desc = [] + current_cites = [] + in_key_readings = False + j += 1 + continue + + # Description line (starts with "Description:") + if clean_stripped.startswith('Description:') and current_sc and not in_key_readings: + desc_text = clean_stripped[len('Description:'):].strip() + if desc_text: + current_desc.append(desc_text) + j += 1 + continue + + # Key Readings marker + if clean_stripped in ('Key Readings:', 'Key Readings'): + in_key_readings = True + j += 1 + continue + + # Citation line + if BULLET_RE.match(stripped) and current_sc: + cite_text = BULLET_RE.sub('', stripped) + current_cites.append(cite_text) + in_key_readings = True # Once we see citations, we're past description + j += 1 + continue + + # Continuation line + if in_key_readings and current_sc and lines[j].startswith(' '): + if current_cites: + current_cites[-1] += ' ' + stripped + j += 1 + continue + + # Description continuation + if current_sc and not in_key_readings: + current_desc.append(stripped) + + j += 1 + + save_current() + return description, sub_clusters + + +def parse_document(lines): + """Parse the full document into Cluster objects.""" + lines = preprocess_lines(lines) + content_start = find_content_start(lines) + boundaries = find_cluster_boundaries(lines, content_start) + + if len(boundaries) != 11: + print(f" WARNING: Expected 11 clusters, found {len(boundaries)}") + + # Compute end boundaries + content_end = find_content_end(lines, boundaries[-1][0]) + cluster_ranges = [] + for i, (line_idx, num, name, annots) in enumerate(boundaries): + if i + 1 < len(boundaries): + end = boundaries[i + 1][0] + else: + end = content_end + cluster_ranges.append((line_idx, end, num, name, annots)) + + clusters = [] + for line_idx, end, num, name, annots in cluster_ranges: + if num <= 10: + # Find Description line (or first content line for clusters like 7) + desc_start = None + for j in range(line_idx + 1, min(line_idx + 5, end)): + stripped_j = lines[j].strip() + if stripped_j == 'Description': + desc_start = j + 1 + break + # Accept first non-blank content line as fallback (Cluster 7 format) + if (stripped_j and not CLUSTER_RE.match(stripped_j) + and not SEPARATOR_RE.match(stripped_j)): + desc_start = j + break + if desc_start is None: + desc_start = line_idx + 1 + + description, toc_names, toc_end = parse_cluster_toc(lines, desc_start, end) + + # Skip blank lines after ToC + sc_start = toc_end + while sc_start < end and not lines[sc_start].strip(): + sc_start += 1 + + sub_clusters = parse_subclusters_standard( + lines, sc_start, end, toc_names, name + ) + + cluster = Cluster( + number=num, name=name, description=description, + annotations=annots, sub_clusters=sub_clusters + ) + else: + # Cluster 11 + description, sub_clusters = parse_cluster_11(lines, line_idx, end) + cluster = Cluster( + number=num, name=name, description=description, + annotations=annots, sub_clusters=sub_clusters + ) + + clusters.append(cluster) + + return clusters + + +# --- Build publications list --- +def build_publications(clusters): + """Convert raw citations into Publication objects.""" + publications = [] + for cluster in clusters: + for sc in cluster.sub_clusters: + for raw_cite in sc.raw_citations: + text, annots = clean_citation_text(raw_cite) + doi = extract_doi(text) + pub = Publication( + sub_cluster=sc.name, + doi=doi or '', + apa_reference=text, # Will be replaced by doi.org lookup if successful + bibtex='', + auto_ref=False, + annotations=annots, + ) + publications.append(pub) + return publications + + +# --- DOI lookup --- +class DOILookup: + def __init__(self, cache_file): + self.cache_file = cache_file + self.cache = {} + self.load_cache() + self.hits = 0 + self.misses = 0 + self.failures = 0 + + def load_cache(self): + if os.path.exists(self.cache_file): + with open(self.cache_file) as f: + self.cache = json.load(f) + print(f" Loaded {len(self.cache)} cached DOI lookups") + + def save_cache(self): + with open(self.cache_file, 'w') as f: + json.dump(self.cache, f, indent=2, ensure_ascii=False) + + def lookup(self, doi): + """Look up DOI via doi.org content negotiation. Returns {apa, bibtex} or None.""" + if doi in self.cache: + self.hits += 1 + return self.cache[doi] + + self.misses += 1 + result = {} + + # Fetch APA reference + apa = self._fetch_formatted(doi, 'text/x-bibliography; style=apa; locale=en-US') + if apa: + result['apa'] = apa.strip() + else: + self.failures += 1 + return None + + # Fetch BibTeX + bibtex = self._fetch_formatted(doi, 'application/x-bibtex') + if bibtex: + result['bibtex'] = bibtex.strip() + else: + result['bibtex'] = '' + + self.cache[doi] = result + # Save cache periodically + if self.misses % 50 == 0: + self.save_cache() + return result + + def _fetch_formatted(self, doi, accept_header): + """Fetch a formatted representation of a DOI.""" + from urllib.parse import quote + url = f'https://doi.org/{quote(doi, safe="/:@!$&()*+,;=-._~")}' + req = urllib.request.Request(url) + req.add_header('Accept', accept_header) + req.add_header('User-Agent', 'FORRT-ClusterParser/1.0 (mailto:info@forrt.org)') + + try: + with urllib.request.urlopen(req, timeout=15) as resp: + return resp.read().decode('utf-8') + except urllib.error.HTTPError as e: + if e.code == 406: + return None # Content negotiation not supported + if e.code == 404: + return None + print(f" HTTP {e.code} for {doi}") + return None + except Exception as e: + print(f" Error fetching {doi}: {e}") + return None + + def print_stats(self): + print(f" DOI lookups: {self.hits} cached, {self.misses} fetched, {self.failures} failed") + + +# --- Sheet writing via gws --- +def gws_run(service, resource, *sub, method, params=None, body=None): + """Run a gws CLI command and return parsed JSON output.""" + cmd = ['gws', service, resource] + cmd.extend(sub) + cmd.append(method) + if params: + cmd.extend(['--params', json.dumps(params)]) + if body: + body_json = json.dumps(body, ensure_ascii=False) + if len(body_json) > 200_000: + # Large payload: write to temp file and use shell + import tempfile + with tempfile.NamedTemporaryFile( + mode='w', suffix='.json', delete=False) as f: + f.write(body_json) + tmp = f.name + shell_cmd = ( + f"gws {service} {resource} {' '.join(sub)} {method} " + f"--params '{json.dumps(params)}' " + f"--json \"$(cat {tmp})\"" + ) + result = subprocess.run( + shell_cmd, shell=True, capture_output=True, text=True) + os.unlink(tmp) + else: + cmd.extend(['--json', body_json]) + result = subprocess.run(cmd, capture_output=True, text=True) + else: + result = subprocess.run(cmd, capture_output=True, text=True) + + # Filter informational keyring message from stderr + stderr = (result.stderr or '').replace( + 'Using keyring backend: keyring\n', '').strip() + + if result.returncode != 0: + print(f" gws error (rc={result.returncode}): {stderr or result.stdout[:500]}") + return None + + # Parse JSON output (skip keyring message line if present) + output = result.stdout + if output.startswith('Using keyring'): + output = output[output.index('\n') + 1:] + try: + return json.loads(output) + except json.JSONDecodeError: + return output + + +def write_sheet_values(sheet_range, values): + """Write values to a Google Sheet range. Batches large writes.""" + BATCH_SIZE = 100 + + for i in range(0, len(values), BATCH_SIZE): + batch = values[i:i + BATCH_SIZE] + row_start = 2 + i # Data starts at row 2 + range_str = f"'{sheet_range}'!A{row_start}" + + result = gws_run( + 'sheets', 'spreadsheets', 'values', method='update', + params={ + 'spreadsheetId': SHEET_ID, + 'range': range_str, + 'valueInputOption': 'RAW', + }, + body={'values': batch}, + ) + if result is None: + print(f" Failed to write batch starting at row {row_start}") + return False + + end_row = row_start + len(batch) - 1 + print(f" Wrote rows {row_start}-{end_row} to {sheet_range}") + time.sleep(0.5) # Avoid API rate limits + + return True + + +def ensure_sheet_rows(sheet_id_num, needed_rows): + """Expand a sheet's grid if it doesn't have enough rows.""" + gws_run( + 'sheets', 'spreadsheets', method='batchUpdate', + params={'spreadsheetId': SHEET_ID}, + body={'requests': [{ + 'updateSheetProperties': { + 'properties': { + 'sheetId': sheet_id_num, + 'gridProperties': {'rowCount': needed_rows + 10}, + }, + 'fields': 'gridProperties.rowCount', + } + }]}, + ) + + +def clear_sheet_data(sheet_name): + """Clear all data rows (keep header) from a sheet.""" + range_str = f"'{sheet_name}'!A2:Z" + gws_run( + 'sheets', 'spreadsheets', 'values', method='clear', + params={'spreadsheetId': SHEET_ID, 'range': range_str}, + body={}, + ) + + +def update_header(sheet_name, headers): + """Update the header row of a sheet.""" + range_str = f"'{sheet_name}'!A1" + gws_run( + 'sheets', 'spreadsheets', 'values', method='update', + params={ + 'spreadsheetId': SHEET_ID, + 'range': range_str, + 'valueInputOption': 'RAW', + }, + body={'values': [headers]}, + ) + + +def add_data_validation(): + """Add dropdown data validation to Sub-Clusters and Publications sheets.""" + # Sheet IDs from the spreadsheet + SUBCLUSTERS_SHEET_ID = 2142431425 + PUBLICATIONS_SHEET_ID = 1999901341 + + requests = [ + # Sub-Clusters!A (Cluster column) -> validated against Clusters!A + { + 'setDataValidation': { + 'range': { + 'sheetId': SUBCLUSTERS_SHEET_ID, + 'startRowIndex': 1, + 'startColumnIndex': 0, + 'endColumnIndex': 1, + }, + 'rule': { + 'condition': { + 'type': 'ONE_OF_RANGE', + 'values': [{'userEnteredValue': '=Clusters!$A$2:$A'}], + }, + 'strict': True, + 'showCustomUi': True, + }, + } + }, + # Publications!A (Sub-Cluster column) -> validated against Sub-Clusters!B + { + 'setDataValidation': { + 'range': { + 'sheetId': PUBLICATIONS_SHEET_ID, + 'startRowIndex': 1, + 'startColumnIndex': 0, + 'endColumnIndex': 1, + }, + 'rule': { + 'condition': { + 'type': 'ONE_OF_RANGE', + 'values': [{'userEnteredValue': "='Sub-Clusters'!$B$2:$B"}], + }, + 'strict': True, + 'showCustomUi': True, + }, + } + }, + ] + + gws_run( + 'sheets', 'spreadsheets', method='batchUpdate', + params={'spreadsheetId': SHEET_ID}, + body={'requests': requests}, + ) + print(" Data validation rules added") + + +# --- Validation --- +def validate(clusters, publications): + """Validate parsed data and print warnings.""" + sc_names = set() + for c in clusters: + for sc in c.sub_clusters: + sc_names.add(sc.name) + + # Check all publication sub-cluster references + invalid = set() + for pub in publications: + if pub.sub_cluster not in sc_names: + invalid.add(pub.sub_cluster) + + if invalid: + print(f" WARNING: {len(invalid)} publication sub-cluster names not in Sub-Clusters sheet:") + for name in sorted(invalid): + print(f" - {name!r}") + + # Check for zero-citation sub-clusters + for c in clusters: + for sc in c.sub_clusters: + if not sc.raw_citations: + print(f" WARNING: No citations for sub-cluster '{sc.name}' in Cluster {c.number}") + + +# --- JSON export for Hugo --- +def _clean_html_entities(text): + """Decode HTML entities in text (e.g. & -> &).""" + import html + return html.unescape(text) if text else text + + +def export_json(clusters, publications): + """Export clusters data as JSON for Hugo to consume.""" + # Build a lookup: (sub_cluster_name) -> list of publications + pub_by_sc = {} + for pub in publications: + pub_by_sc.setdefault(pub.sub_cluster, []).append(pub) + + data = {"clusters": []} + for c in clusters: + cluster_obj = { + "number": c.number, + "name": c.name, + "description": c.description, + "sub_clusters": [], + } + for sc in c.sub_clusters: + pubs = pub_by_sc.get(sc.name, []) + sc_obj = { + "name": sc.name, + "description": sc.description, + "publications": [ + { + "doi": p.doi, + "apa": _clean_html_entities(p.apa_reference), + "auto_ref": p.auto_ref, + } + for p in pubs + ], + } + cluster_obj["sub_clusters"].append(sc_obj) + data["clusters"].append(cluster_obj) + + # Write to data/ directory (relative to repo root) + repo_root = os.path.dirname(SCRIPT_DIR) + out_path = os.path.join(repo_root, 'data', 'clusters_v4.json') + with open(out_path, 'w', encoding='utf-8') as f: + json.dump(data, f, indent=2, ensure_ascii=False) + print(f" Wrote {out_path}") + print(f" {len(data['clusters'])} clusters, " + f"{sum(len(c['sub_clusters']) for c in data['clusters'])} sub-clusters, " + f"{sum(len(p) for c in data['clusters'] for p in [sc['publications'] for sc in c['sub_clusters']])} publications") + + +# --- Main --- +def main(): + parser = argparse.ArgumentParser(description='Parse FORRT Clusters GDoc to GSheet') + parser.add_argument('--dry-run', action='store_true', + help='Parse only, print stats, no DOI lookups or sheet writes') + parser.add_argument('--skip-doi', action='store_true', + help='Skip DOI lookups, use raw text from doc') + parser.add_argument('--cache-file', default=DEFAULT_CACHE, + help='DOI cache file path') + parser.add_argument('--export-json', action='store_true', + help='Export clusters data as JSON for Hugo (data/clusters_v4.json)') + parser.add_argument('--json-only', action='store_true', + help='Only export JSON (skip sheet writing)') + args = parser.parse_args() + + # 1. Fetch and parse + print("=== Fetching document ===") + raw_lines = fetch_document() + + print("\n=== Parsing document ===") + clusters = parse_document(raw_lines) + + # 2. Summary + total_sc = sum(len(c.sub_clusters) for c in clusters) + publications = build_publications(clusters) + dois_found = sum(1 for p in publications if p.doi) + + print(f"\n=== Parsing summary ===") + for c in clusters: + cite_count = sum(len(sc.raw_citations) for sc in c.sub_clusters) + print(f" Cluster {c.number}: {c.name}") + print(f" {len(c.sub_clusters)} sub-clusters, {cite_count} citations") + print(f"\n Total: {len(clusters)} clusters, {total_sc} sub-clusters, " + f"{len(publications)} publications ({dois_found} with DOIs)") + + # 3. Validate + print("\n=== Validating ===") + validate(clusters, publications) + + if args.dry_run: + print("\n=== Dry run complete ===") + return + + # 4. DOI lookups + if not args.skip_doi: + print(f"\n=== Looking up {dois_found} DOIs via doi.org ===") + doi_lookup = DOILookup(args.cache_file) + + for i, pub in enumerate(publications): + if not pub.doi: + continue + result = doi_lookup.lookup(pub.doi) + if result: + pub.apa_reference = result['apa'] + pub.bibtex = result.get('bibtex', '') + pub.auto_ref = True + if (i + 1) % 100 == 0: + print(f" Progress: {i + 1}/{len(publications)}") + + doi_lookup.save_cache() + doi_lookup.print_stats() + + auto_count = sum(1 for p in publications if p.auto_ref) + print(f" {auto_count}/{len(publications)} publications with auto-ref") + + # 5. Export JSON for Hugo + if args.export_json or args.json_only: + print("\n=== Exporting JSON for Hugo ===") + export_json(clusters, publications) + + if args.json_only: + print("\n=== JSON-only mode, skipping sheet write ===") + return + + # 6. Write to Google Sheet + print("\n=== Writing to Google Sheet ===") + + # Update headers (annotations only on Publications) + print(" Updating headers...") + update_header('Clusters', ['Name', 'Explanation']) + update_header('Sub-Clusters', ['Cluster', 'Name', 'Explanation']) + update_header('Publications', ['Sub-Cluster', 'DOI', 'APA Reference', + 'BibTex reference', 'auto-ref', 'annotations']) + + # Clear existing data + print(" Clearing existing data...") + clear_sheet_data('Clusters') + clear_sheet_data('Sub-Clusters') + clear_sheet_data('Publications') + + # Write Clusters + print(" Writing Clusters...") + cluster_rows = [[c.name, c.description] for c in clusters] + write_sheet_values('Clusters', cluster_rows) + + # Write Sub-Clusters + print(" Writing Sub-Clusters...") + sc_rows = [] + for c in clusters: + for sc in c.sub_clusters: + sc_rows.append([sc.cluster_name, sc.name, sc.description]) + write_sheet_values('Sub-Clusters', sc_rows) + + # Write Publications (expand grid if needed) + print(" Writing Publications...") + PUBLICATIONS_SHEET_ID = 1999901341 + ensure_sheet_rows(PUBLICATIONS_SHEET_ID, len(publications) + 2) + pub_rows = [] + for pub in publications: + pub_rows.append([ + pub.sub_cluster, + pub.doi, + pub.apa_reference, + pub.bibtex, + 'TRUE' if pub.auto_ref else 'FALSE', + pub.annotations, + ]) + write_sheet_values('Publications', pub_rows) + + # 6. Data validation + print("\n=== Adding data validation ===") + add_data_validation() + + print("\n=== Done ===") + print(f" Sheet: https://docs.google.com/spreadsheets/d/{SHEET_ID}") + + +if __name__ == '__main__': + main() From 9ad47b9c9ddd8ed03462ce5e53381080452c028d Mon Sep 17 00:00:00 2001 From: Lukas Wallrich Date: Sun, 22 Mar 2026 22:34:15 +0000 Subject: [PATCH 02/11] Disable site-wide search (replaced by clusters page search) The clusters page now has its own full-text search that covers clusters, sub-clusters, and all references. The site-wide Academic search is redundant and has been disabled. Co-Authored-By: Claude Opus 4.6 (1M context) --- config/_default/params.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/_default/params.toml b/config/_default/params.toml index bc462b219d5..e530f1ff2e8 100644 --- a/config/_default/params.toml +++ b/config/_default/params.toml @@ -242,7 +242,7 @@ plugins_js = [] # 0: No search engine # 1: Academic (built-in) # 2: Algolia (https://www.algolia.com) - engine = 1 + engine = 0 # Configuration of Algolia search engine. # Paste the values from your Algolia dashboard. From 9b9bdc4feb85e1c6c11cbd8c04ec510e880feddf Mon Sep 17 00:00:00 2001 From: Lukas Wallrich Date: Sun, 22 Mar 2026 22:42:14 +0000 Subject: [PATCH 03/11] Revert "Disable site-wide search (replaced by clusters page search)" This reverts commit 9ad47b9c9ddd8ed03462ce5e53381080452c028d. --- config/_default/params.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/_default/params.toml b/config/_default/params.toml index e530f1ff2e8..bc462b219d5 100644 --- a/config/_default/params.toml +++ b/config/_default/params.toml @@ -242,7 +242,7 @@ plugins_js = [] # 0: No search engine # 1: Academic (built-in) # 2: Algolia (https://www.algolia.com) - engine = 0 + engine = 1 # Configuration of Algolia search engine. # Paste the values from your Algolia dashboard. From 671781c35d11bf189c204179121e9afcaf811146 Mon Sep 17 00:00:00 2001 From: richarddushime Date: Mon, 23 Mar 2026 18:58:20 +0100 Subject: [PATCH 04/11] enhancement:clusters page --- assets/scss/custom.scss | 556 +++++++++++++++++++- content/clusters/1-hero.md | 56 -- content/clusters/cluster1.md | 216 -------- content/clusters/cluster2.md | 162 ------ content/clusters/cluster3.md | 176 ------- content/clusters/cluster4.md | 212 -------- content/clusters/cluster5.md | 183 ------- content/clusters/cluster6.md | 201 ------- content/clusters/cluster7.md | 359 ------------- content/clusters/clusters-data.md | 21 - content/clusters/index.md | 11 +- content/clusters/intro-clusters.md | 88 ---- layouts/clusters/list.html | 44 ++ layouts/clusters/single.html | 53 ++ layouts/partials/clusters/all_clusters.html | 147 ++++++ layouts/partials/clusters/intro.html | 78 +++ layouts/partials/custom_js.html | 6 +- layouts/shortcodes/clusters_display.html | 367 ------------- static/js/clusters-page.js | 176 +++++++ 19 files changed, 1041 insertions(+), 2071 deletions(-) delete mode 100644 content/clusters/1-hero.md delete mode 100644 content/clusters/cluster1.md delete mode 100644 content/clusters/cluster2.md delete mode 100644 content/clusters/cluster3.md delete mode 100644 content/clusters/cluster4.md delete mode 100644 content/clusters/cluster5.md delete mode 100644 content/clusters/cluster6.md delete mode 100644 content/clusters/cluster7.md delete mode 100644 content/clusters/clusters-data.md delete mode 100644 content/clusters/intro-clusters.md create mode 100644 layouts/clusters/list.html create mode 100644 layouts/clusters/single.html create mode 100644 layouts/partials/clusters/all_clusters.html create mode 100644 layouts/partials/clusters/intro.html delete mode 100644 layouts/shortcodes/clusters_display.html create mode 100644 static/js/clusters-page.js diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index 4cc2c5d8dcb..3b3e9245f14 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -32,13 +32,43 @@ /* Clusters v4 page styles */ /* -------------------------------------------------- */ +/* Sticky offsets: fallbacks before clusters-page.js sets --clusters-sticky-offset inline */ .clusters-layout { margin-top: 0.5rem; + --clusters-sticky-offset: 70px; + --clusters-sticky-gap: 0px; + --clusters-controls-height: 0px; +} + +@media screen and (max-width: 1200px) { + .clusters-layout { + --clusters-sticky-offset: 50px; + } +} + +@media (min-width: 992px) and (max-width: 1350px) { + .clusters-layout { + --clusters-sticky-offset: 130px; + } +} + +.clusters-controls { + position: sticky; + top: calc(var(--clusters-sticky-offset) + env(safe-area-inset-top, 0px) + var(--clusters-sticky-gap)); + z-index: 1020; + display: grid; + gap: 0.45rem; + background: #fefdf6; + padding: 0.5rem; + border: 1px solid #e9ecef; + border-radius: 8px; + box-shadow: 0 4px 10px rgba(0, 0, 0, 0.05); } /* ---- Mobile nav toggle ---- */ .clusters-mobile-toggle { width: 100%; + margin-top: 0; text-align: left; font-size: 0.9rem; padding: 0.5rem 1rem; @@ -56,7 +86,7 @@ display: none; } -@media (min-width: 1200px) { +@media (min-width: 992px) { .clusters-sidebar { display: block; } @@ -68,8 +98,14 @@ .clusters-sidebar-inner { position: sticky; - top: 60px; - max-height: calc(100vh - 80px); + top: calc( + var(--clusters-sticky-offset) + + env(safe-area-inset-top, 0px) + + var(--clusters-sticky-gap) + + var(--clusters-controls-height) + + 8px + ); + max-height: calc(100vh - var(--clusters-sticky-offset) - 20px); overflow-y: auto; padding: 0.75rem; background: #f8f9fa; @@ -79,6 +115,12 @@ } .sidebar-header { + position: sticky; + top: 0; + z-index: 2; + background: #f8f9fa; + padding: 0.15rem 0.1rem 0.45rem; + border-bottom: 1px solid #e9ecef; font-size: 0.75rem; font-weight: 700; text-transform: uppercase; @@ -192,6 +234,10 @@ } /* ---- Search bar ---- */ +.clusters-search-bar { + position: relative; +} + .clusters-search-bar .form-control { font-size: 0.9rem; padding: 0.5rem 0.75rem; @@ -229,23 +275,6 @@ color: #111; } -.search-result-context { - display: block; - font-size: 0.7rem; - color: #888; - margin-bottom: 0.15rem; -} - -.search-snippet { - font-size: 0.78rem; - color: #444; -} - -.search-snippet mark { - background: #fff3cd; - padding: 0 0.1em; -} - .search-no-results, .search-more { padding: 0.5rem 0.75rem; font-size: 0.78rem; @@ -339,29 +368,218 @@ /* ---- Responsive ---- */ @media (max-width: 1199px) { + .clusters-controls { + padding: 0.4rem; + } + + .cluster-search-results { + max-height: 42vh; + } + + .cluster-section { + padding: 1rem 0.75rem; + } + + .cluster-tabs .nav-link { + font-size: 0.72rem; + padding: 0.35rem 0.55rem; + } +} + +@media (max-width: 991px) { .clusters-sidebar-inner { position: static; max-height: 50vh; margin-bottom: 1rem; } + .sidebar-header { + position: static; + border-bottom: 0; + padding: 0; + } + + .clusters-sidebar.sidebar-open { + background: #fff; + border: 1px solid #e9ecef; + border-radius: 8px; + padding: 0.5rem; + margin-bottom: 0.75rem; + } + + .cluster-tabs { + flex-wrap: nowrap; + overflow-x: auto; + overflow-y: hidden; + -webkit-overflow-scrolling: touch; + scrollbar-width: thin; + } + + .cluster-tabs .nav-item { + max-width: none; + } + + .cluster-tabs .nav-link { + white-space: nowrap; + word-break: normal; + } + + .cluster-tab-content { + padding: 0.95rem 0.25rem; + } +} + +@media (max-width: 768px) { + .clusters-controls { + border-radius: 6px; + box-shadow: 0 2px 8px rgba(0, 0, 0, 0.05); + } + + .clusters-search-bar .form-control { + font-size: 0.86rem; + padding: 0.46rem 0.62rem; + } + + .cluster-search-results { + max-height: 38vh; + } + .cluster-section { - padding: 1rem 0.75rem; + padding: 0.9rem 0.65rem; + border-radius: 7px; + } + + .cluster-title { + align-items: flex-start; + gap: 0.35rem; + } + + .cluster-number { + margin-top: 0.1rem; + } + + .cluster-stats { + display: block; + margin-top: 0.2rem; + } + + .publication-list { + padding-left: 1rem; + } + + .publication-item { + margin-bottom: 0.2rem; + } +} + +@media (max-width: 576px) { + .clusters-controls { + padding: 0.35rem; + margin-bottom: 0.6rem !important; + gap: 0.35rem; + } + + .cluster-title { + font-size: 0.98rem; + line-height: 1.35; + } + + .cluster-description { + font-size: 0.78rem; + } + + .publication-item { + font-size: 0.75rem; + line-height: 1.45; } .cluster-tabs .nav-link { font-size: 0.68rem; - padding: 0.3rem 0.45rem; + padding: 0.32rem 0.48rem; } + } -@media (max-width: 576px) { +@media (max-width: 420px) { + .clusters-layout { + margin-top: 0.25rem; + } + + .clusters-controls { + padding: 0.3rem; + border-radius: 5px; + } + + .clusters-search-bar .form-control { + font-size: 0.82rem; + padding: 0.42rem 0.55rem; + } + + .cluster-search-results { + max-height: 34vh; + } + + .clusters-mobile-toggle { + font-size: 0.82rem; + padding: 0.45rem 0.8rem; + } + + .cluster-section { + padding: 0.8rem 0.55rem; + margin-bottom: 0.6rem; + } + .cluster-title { - font-size: 1rem; + font-size: 0.92rem; + } + + .cluster-number { + width: 1.45em; + height: 1.45em; + } + + .cluster-stats { + font-size: 0.66rem; + } + + .cluster-tabs .nav-link { + min-height: 2rem; + padding: 0.34rem 0.44rem; + } + + .sc-heading { + font-size: 0.98rem; + } +} + +@media (max-width: 390px) { + .clusters-mobile-toggle { + margin-top: 0.45rem; + } + + .cluster-tabs { + scroll-padding-left: 0.25rem; + } + + .cluster-tabs .nav-link { + font-size: 0.66rem; + min-height: 1.9rem; + border-radius: 3px 3px 0 0; + } + + .cluster-tab-content { + padding: 0.8rem 0.2rem; } .publication-item { font-size: 0.72rem; + line-height: 1.4; + } + + .clusters-back-to-top { + width: 2.35rem; + height: 2.35rem; + font-size: 0.85rem; } } @@ -1025,3 +1243,293 @@ article.article:has(table) .article-container { justify-content: center !important; } } + +/* -------------------------------------------------- */ +/* Clusters Intro Section Styles */ +/* -------------------------------------------------- */ + +.clusters-intro { + margin-bottom: 0; +} + +/* Main introductory paragraphs */ +.intro-content { + line-height: 1.6; +} + +.intro-paragraph { + font-size: 0.95rem; + color: #444; + margin-bottom: 1.25rem; + line-height: 1.6; +} + +.intro-note { + font-size: 0.9rem; + color: #666; + background: rgba(255, 235, 205, 0.3); + padding: 0.75rem 1rem; + border-left: 3px solid #ff9800; + border-radius: 4px; + margin: 1.5rem 0; + font-style: italic; +} + +/* Numbered clusters list */ +.intro-clusters-list { + margin: 1.5rem 0 1.5rem 0; +} + +.clusters-numbered-list { + font-size: 0.9rem; + color: #555; + padding-left: 1.5rem; + line-height: 1.7; +} + +.clusters-numbered-list li { + margin-bottom: 0.65rem; +} + +.clusters-numbered-list li::marker { + color: #6070a0; + font-weight: 600; +} + +/* Image section */ +.intro-image-wrapper { + margin: 1.25rem 0 0.5rem; + text-align: center; + padding: 0.85rem 0 0.6rem; + background: linear-gradient(135deg, rgba(202, 207, 220, 0.08) 0%, rgba(212, 228, 217, 0.08) 100%); + border-radius: 12px; +} + +.intro-figure { + margin: 0 auto; + display: block; + width: 100%; + max-width: 100%; +} + +.intro-image { + width: 100%; + max-width: 100%; + height: auto; + border-radius: 10px; + box-shadow: 0 8px 24px rgba(0, 0, 0, 0.12), 0 2px 6px rgba(0, 0, 0, 0.08); + border: 2px solid rgba(255, 255, 255, 0.8); + background: white; + padding: 4px; + display: block; +} + +.intro-figcaption { + font-size: 0.95rem; + color: #666; + margin-top: 0.55rem; + margin-bottom: 0; + font-weight: 500; + font-style: normal; +} + +/* Use full container width on large screens (theme XL container = 1200px) */ +@media (min-width: 992px) { + .intro-image-wrapper { + padding: 1rem 0 0.75rem; + } + + .intro-image { + padding: 6px; + } +} + +@media (min-width: 1200px) { + .intro-image-wrapper { + margin: 1.35rem 0 0.55rem; + padding: 1.15rem 0 0.7rem; + } + + .intro-figcaption { + font-size: 1rem; + margin-top: 0.65rem; + } +} + +/* Syllabus section */ +.intro-syllabus { + margin-top: 1rem; + margin-bottom: 0; + padding: 0.85rem 1.25rem 1.15rem; + background: #f8f9fa; + border-radius: 8px; + border: 1px solid #e9ecef; +} + +.syllabus-heading { + font-size: 1.1rem; + font-weight: 700; + color: #333; + margin-bottom: 0.75rem; +} + +.syllabus-text { + font-size: 0.95rem; + color: #555; + margin-bottom: 1rem; + line-height: 1.5; +} + +.syllabus-links { + display: flex; + flex-wrap: wrap; + gap: 0.75rem; +} + +.syllabus-link { + display: inline-flex; + align-items: center; + gap: 0.5rem; + padding: 0.6rem 1rem; + background: white; + border: 1px solid #dee2e6; + border-radius: 6px; + color: #1c7ed6; + text-decoration: none; + font-size: 0.9rem; + font-weight: 500; + transition: all 0.2s ease; +} + +.syllabus-link:hover { + background: #ecf2ff; + border-color: #1c7ed6; + color: #0c5ba8; + text-decoration: none; + box-shadow: 0 2px 6px rgba(28, 126, 214, 0.1); +} + +.link-icon { + font-size: 0.95rem; +} + +/* Responsive adjustments for clusters intro */ +@media (max-width: 768px) { + .intro-paragraph { + font-size: 0.9rem; + } + + .clusters-numbered-list { + font-size: 0.85rem; + } + + .intro-syllabus { + margin-top: 0.85rem; + padding: 0.75rem 1rem 1rem; + } + + .syllabus-links { + gap: 0.5rem; + } + + .syllabus-link { + padding: 0.5rem 0.8rem; + font-size: 0.85rem; + } + + .intro-image-wrapper { + margin: 1.1rem 0 0.45rem; + padding: 0.65rem 0 0.5rem; + } + + .intro-image { + box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1); + } + + .intro-figcaption { + font-size: 0.9rem; + } +} + +@media (max-width: 480px) { + .intro-image-wrapper { + margin: 1rem 0 0.35rem; + padding: 0.5rem 0 0.4rem; + } + + .intro-figure { + max-width: 100%; + } +} + +/* -------------------------------------------------- */ +/* Clusters Page Section Styles */ +/* -------------------------------------------------- */ + +.clusters-intro-section { + background: linear-gradient(to bottom, #fefdf6 0%, #f9f8f5 100%); + padding: 0.5rem 0 0.5rem; + margin: 0.15rem 0 0; +} + +.clusters-display-section { + background: white; + padding: 0.75rem 0 2rem; + margin: 0 0 1.5rem; + border-top: 1px solid #e9ecef; + border-bottom: 1px solid #e9ecef; +} + +.clusters-back-to-top { + position: fixed; + right: 1.25rem; + bottom: 1.25rem; + z-index: 1050; + display: inline-flex; + align-items: center; + justify-content: center; + border: none; + border-radius: 999px; + background: #2f3f66; + color: #fff; + width: 2.75rem; + height: 2.75rem; + padding: 0; + font-size: 1rem; + line-height: 1; + box-shadow: 0 8px 18px rgba(47, 63, 102, 0.3); + cursor: pointer; + opacity: 0; + visibility: hidden; + transform: translateY(8px); + transition: opacity 0.2s ease, transform 0.2s ease, visibility 0.2s ease, background 0.2s ease; +} + +.clusters-back-to-top i { + line-height: 1; +} + +.clusters-back-to-top:hover { + background: #233456; +} + +.clusters-back-to-top:focus { + outline: 2px solid #1c7ed6; + outline-offset: 2px; +} + +.clusters-back-to-top.is-visible { + opacity: 1; + visibility: visible; + transform: translateY(0); +} + +@media (max-width: 768px) { + .clusters-back-to-top { + right: calc(0.85rem + env(safe-area-inset-right, 0px)); + bottom: calc(0.85rem + env(safe-area-inset-bottom, 0px)); + width: 2.5rem; + height: 2.5rem; + font-size: 0.92rem; + } +} diff --git a/content/clusters/1-hero.md b/content/clusters/1-hero.md deleted file mode 100644 index 5494b69b932..00000000000 --- a/content/clusters/1-hero.md +++ /dev/null @@ -1,56 +0,0 @@ -+++ -# Hero widget. -widget = "hero_welcome" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 1 # Order that this section will appear. - -title = "Framework for
Open and
Reproducible
Research
Training" - -# Hero image (optional). Enter filename of an image in the `static/img/` folder. -hero_media = "FORRT.svg" -hero_media_alttext = "Logo of FORRT is a fort." -# [design.spacing] -# # Customize the section spacing. Order is top, right, bottom, left. -# padding = ["20px", "0", "20px", "0"] - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "#fefdf6" - - # Background gradient. - # gradient_start = "#4bb4e3" - # gradient_end = "#2b94c3" - - # Background image. - # image = "FORRT.svg" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -# Call to action links (optional). -# Display link(s) by specifying a URL and label below. Icon is optional for `[cta]`. -# Remove a link/note by deleting a cta/note block. -# [cta] -# url = "https://sourcethemes.com/academic/docs/install/" -# label = "Get Started" -# icon_pack = "fas" -# icon = "download" - -# [cta_alt] -# url = "https://sourcethemes.com/academic/" -# label = "View Documentation" - -# Note. An optional note to show underneath the links. -# [cta_note] -# label = 'Latest release' -+++ diff --git a/content/clusters/cluster1.md b/content/clusters/cluster1.md deleted file mode 100644 index 034f78586d1..00000000000 --- a/content/clusters/cluster1.md +++ /dev/null @@ -1,216 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 10 # Order that this section will appear. - -title = "Cluster 1: Reproducibility Crisis and Credibility Revolution" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "red" - color = "#cacfdc" # greenish - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1rem;" - - # CSS class. - css_class = "" -+++ - -### Description - -Attainment of foundational knowledge on the emergence of, and importance of, reproducible and open research (i.e., grounding the motivations and theoretical underpinnings of Open and Reproducible Science). Integration with field specific content (i.e., grounded in the history of replicability). There are 6 sub-clusters which aim to further parse the learning and teaching process: - -* History of the reproducibility crisis & credibility revolution. -* Exploratory and confirmatory analyses. -* Questionable research practices and their prevalence. -* Proposed improvement science initiatives on statistics, measurement, teaching, data sharing, code sharing, pre-registration, replication. -* Ongoing debates (e.g., incentives for and against open science). -* Ethical considerations for improved practices. - -
- - - -
-

- -## History of the reproducibility crisis & credibility revolution - -* Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature News, 533(7604), 452. doi: https://doi.org/10.1038/533452a - -* Baker, M. (2016). Is there a reproducibility crisis? Nature, 533(7604), 3–5. doi: https://doi.org/10.1038/d41586-019-00067-3 - -* Chambers, C. (2017). The seven deadly sins of psychology: A manifesto for reforming the culture of scientific practice. Princeton University Press. -http://dx.doi.org/10.1515/9781400884940 - -* Crüwell, S., van Doorn, J., Etz, A., Makel, M. C., Moshontz, H., Niebaum, J., … SchulteMecklenbeck, M. (2018, November 16). 7 easy steps to open science: An annotated reading list. https://doi.org/10.31234/osf.io/cfzyx - -* Edwards, M. A., & Roy, S. (2016). Academic research in the 21st century: Maintaining scientific integrity in a climate of perverse incentives and hypercompetition. Environmental Engineering Science, 34(1), 51-61. DOI: https://doi.org/10.1089/ees.2016.0223 - -* Merton, R., K. (1968). The Matthew effect in science. Science, 159(3810), 56-63. -10.1126/science.159.3810.56 - -* Merton, R., K. (1988). The Matthew Effect in Science, II: Cumulative Advantage and the Symbolism of Intellectual Property. ISIS, 79(4), 606-623. 10.1086/354848 - -* Munafo, M. R., et al. (2017). A manifesto for reproducible science. Nature Human Behaviour, 1, 0021. DOI: 10.0138/s41562-016-0021 - -* Vazire, S. (2018). Implications of the Credibility Revolution for Productivity, Creativity, and Progress. Perspectives on Psychological Science, 13(4), 411-417. -https://doi.org/10.1177/1745691617751884 - -
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- -## Exploratory and confirmatory analyses - -***Confirmatory analyses refer to tests of hypotheses that are formulated prior to data collection. Exploratory analyses refer to everything else.*** - -* Chambers, C. (2017). The seven deadly sins of psychology: A manifesto for reforming the culture of scientific practice. Princeton University Press. -http://dx.doi.org/10.1515/9781400884940 - -* Lin, W., & Green, D. P. (2016). Standard operating procedures: A safety net for pre-analysis plans. PS: Political Science & Politics, 49(3), 495-500. - -* Wagenmakers, E.-J., Wetzels, R., Borsboom, D., van der Mass, H. L. J., & Kievit, R. A. (2012). An agenda for purely confirmatory research. Perspectives on Psychological Science, 7(6), 632–638. doi:10.1177/1745691612463078 - -* Wagenmakers , E.-J., Dutilh, G., & Sarafoglou, A. (2018). The Creativity-Verification Cycle in Psychological Science: New Methods to Combat Old Idols. Perspectives on Psychological Science, 13(4), 418–427. https://doi.org/10.1177/1745691618771357 - -
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- -## Questionable research practices and their prevalence - -***The ways in which researchers engage in behaviors and decision-making that increase the probability of their (consciously or unconsciously) desired result.*** - -* Gelman, A., & Loken, E. (2013). The garden of forking paths: Why multiple comparisons can be a problem, even when there is no “fishing expedition” or “p-hacking” and the research hypothesis was posited ahead of time. Unpublished manuscript. http://www.stat.columbia.edu/~gelman/research/unpublished/p_hacking.pdf - -* John, L. K., Loewenstein, G., & Prelec, D. (2012). Measuring the prevalence of questionable research practices with incentives for truth telling. Psychological Science, 23(5), 524-532. https://doi.org/10.1177/0956797611430953 - -* Simmons, J. P., Nelson, L. D., & Simonsohn, U. (2011). False-Positive Psychology: Undisclosed Flexibility in Data Collection and Analysis Allows Presenting Anything as Significant. Psychological Science, 22(11), 1359–1366.https://doi.org/10.1177/0956797611417632 - -* Smaldino, P. E., & McElreath, R. (2016). The natural selection of bad science. Royal Society open science, 3(9), 160384.https://doi.org/10.1098/rsos.160384 - -* Wicherts, J. M., Veldkamp, C. L., Augusteijn, H. E., Bakker, M., Van Aert, R. C., & Van Assen, M. A. (2016). Degrees of freedom in planning, running, analyzing, and reporting psychological studies: A checklist to avoid p-hacking. Frontiers in psychology, 7. - -
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- -## Proposed improvement science initiatives on statistics, measurement, teaching, data sharing, code sharing, pre-registration, replication - -***Published checklists and other resources that can be used to shift behavior more toward improved practices.*** - -* Crüwell, S., van Doorn, J., Etz, A., Makel, M. C., Moshontz, H., Niebaum, J., … SchulteMecklenbeck, M. (2018, November 16). 7 easy steps to open science: An annotated reading list. https://doi.org/10.31234/osf.io/cfzyx - -* Lindsay (2020) Seven steps toward transparency and replicability in psychological science. Canadian Psychology/Psychologie canadienne. - -* Ioannidis, J. P., Munafo, M. R., Fusar-Poli, P., Nosek, B. A., & David, S. P. (2014). Publication and other reporting biases in cognitive sciences: detection, prevalence, and prevention. Trends in cognitive sciences, 18(5), 235-241. - -* Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., … Nosek, B. A. (2018). Many Labs 2: Investigating Variation in Replicability Across Samples and Settings. Advances in Methods and Practices in Psychological Science, 1(4), 443–490. https://doi.org/10.1177/2515245918810225 - -* Munafo, M. R., et al. (2017). A manifesto for reproducible science. Nature Human Behaviour, 1, 0021. DOI: 10.0138/s41562-016-0021 - -* Peng, R. (2015). The reproducibility crisis in science: A statistical counterattack. Significance, 12(3). https://doi.org/10.1111/j.1740-9713.2015.00827.x - - -
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- -## Ongoing debates (e.g., incentives for and against open science) - -* Bahlai et al. (2019). Open science isn't always open to all scientists. American Scientist, 107(2), 78. DOI: https://doi.org/10.1511/2019.107.2.78 - -* Chen, X., Dallmeier-Tiessen, S., Dasler, R., Feger, S., Fokianos, P., Gonzalez, J. B., ... & Rodriguez, D. R. et al. (2019). Open is not enough. Nature : Physics, 15 (2), 113-119. https://doi.org/10.1038/s41567-018-0342-2 - -* Drummond, C. (2018).; Reproducible research: a minority opinion. Journal of Experimental & Theoretical Artificial Intelligence, 30(1), 1-11. https://doi.org/10.1080/0952813X.2017.1413140 - -* Fanelli, D. (2018). Opinion: Is science really facing a reproducibility crisis, and do we need it to? Proceedings of the National Academy of Sciences, 115(11), 2628-2631. https://doi.org/10.1073/pnas.1708272114 - -* Fanelli, D., & Ioannidis, J. P. (2013). US studies may overestimate effect sizes in softer research. Proceedings of the National Academy of Sciences, 110(37), 15031-15036. https://doi.org/10.1073/pnas.1302997110 - -* Fell, M. J. (2019). The economic impacts of open science: A rapid evidence assessment. Publications, 7(3), 46. https://doi.org/10.3390/publications7030046 - -* Pashler, H., & Harris, C. R. (2012). Is the replicability crisis overblown? Three arguments examined. Perspectives on Psychological Science, 7, 531‑536. https://doi.org/10.1177/1745691612463401 - -
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- -## Ethical considerations for improved practices - -* Brabeck, M. M. (2021). Open science and feminist ethics: Promises and challenges of open access. Psychology of Women Quarterly, 45(4), 457-474. https://doi.org/10.1177/03616843211030926 - -* Bol, T., de Vaan, M., & van de Rijt, A. (2018). The Matthew effect in science funding. Proceedings of the National Academy of Sciences, 115(19), 4887-4890. https://doi.org/10.1073/pnas.1719557115 - -* Chopik, W. J., Bremner, R. H., Defever, A. M., & Keller, V. N. (2018). How (and whether) to teach undergraduates about the replication crisis in psychological science. Teaching of Psychology, 45(2), 158–163. https://doi.org/10.1177/0098628318762900 - -* Edwards, M. A., & Roy, S. (2016). Academic research in the 21st century: Maintaining scientific integrity in a climate of perverse incentives and hypercompetition. Environmental Engineering Science, 34(1), 51-61. DOI: https://doi.org/10.1089/ees.2016.0223 - -* Fell, M. J. (2019). The economic impacts of open science: A rapid evidence assessment. Publications, 7(3), 46. https://doi.org/10.3390/publications7030046 - -* Jones, NL. (2007). A code of ethics for the life sciences. Science and Engineering Ethics, 13, 25-43. DOI:https://doi.org/ 0.1007/s11948-006-0007-x - -
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diff --git a/content/clusters/cluster2.md b/content/clusters/cluster2.md deleted file mode 100644 index 21c7a9e994f..00000000000 --- a/content/clusters/cluster2.md +++ /dev/null @@ -1,162 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 10 # Order that this section will appear. - -title = "Cluster 2: Conceptual and Statistical Knowledge" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "red" - color = "#eadce6" # greenish - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1rem;" - - # CSS class. - css_class = "" -+++ - -### Description - -Attainment of a grounding in fundamental statistics, measurement, and its implications encompassing conceptual knowledge, application, interpretation and communication of statistical analyses. There are 5 sub-clusters which aim to further parse the learning and teaching process: - -* The logic of null hypothesis testing, p-values, Type I and II errors (and when and why they might happen). -* Limitations and benefits of NHST, Bayesian and Likelihood approaches. -* Effect sizes, Statistical power, Confidence Intervals. -* Research Design, Sample Methods, and its implications for inferences. -* Questionable measurement practices (QMPs), validity and reliability issues. - -
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- -## The logic of null hypothesis testing, p-values, Type I and II errors (and when and why they might happen). - -* Banerjee, A., Chitnis, UB., Jadhav, SL., Bhawalkar, JS., Chaudhury, S. (2009). Hypothesis testing, type I and type II errors. Industrial Psychiatry Journal, 18(2), 127-131. https://doi.org/10.1111/j.1740-9713.2015.00827.x - -* Gelman, A., & Carlin, J. (2014). Beyond power calculations: Assessing Type S (sign) and Type M (magnitude) errors. Perspectives on Psychological Science, 9(6), 641-651. doi: 10.1177/1745691614551642 - -* Lakens, D. Improving your statistical inferences. Online course. https://www.coursera.org/learn/statistical-inferences - - -
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- -## Limitations and benefits of NHST, Bayesian and Likelihood approaches. - -* Cumming, G. (2014). The new statistics: Why and how. Psychological Science, 25(1), 7-29. https://doi.org/10.1177/0956797613504966 - -* Etz, A., Gronau, Q.F., Dablander, F. et al. (2018). How to become a Bayesian in eight easy steps: An annotated reading list. Psychonomic Bulletin Review, 25, 219–234. https://doi.org/10.3758/s13423-017-1317-5 - -* Greenland, S., Senn, S. J., Rothman, K. J., Carlin, J. B., Poole, C., Goodman, S. N., & Altman, D. G. (2016). Statistical tests, p values, confidence intervals, and power: Aa guide to misinterpretations. European Journal of Epidemiology, 31(4), 337–50. http://doi.org/10.1007/s10654-016-0149-3 - -* Nuzzo, R. (2014). Statistical errors: P values, the ‘gold standard’ of statistical validity, are not as reliable as many scientists assume. Nature, 506(7487), 150-152. doi:10.1038/506150a - -* Wagenmakers , E.-J., Dutilh, G., & Sarafoglou, A. (2018). The Creativity-Verification Cycle in Psychological Science: New Methods to Combat Old Idols. Perspectives on Psychological Science, 13(4), 418–427. https://doi.org/10.1177/1745691618771357 - -
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- -## Effect sizes, Statistical power, Confidence Intervals. - -* Brysbaert, M. and Stevens, M. (2018). Power analysis and effect size in mixed effects models: A Tutorial. Journal of Cognition, 1(1): 9, pp. 1–20, DOI: https://doi.org/10.5334/joc.10 - -* Button, K. S., Ioannidis, J. P., Mokrysz, C., Nosek, B. A., Flint, J., Robinson, E. S., & Munafò, M. R. (2013). Power failure: why small sample size undermines the reliability of neuroscience. Nature Reviews Neuroscience, 14(5), 365-376. https://doi.org/10.1038/nrn3475 - -* Greenland, S., Senn, S. J., Rothman, K. J., Carlin, J. B., Poole, C., Goodman, S. N., & Altman, D. G. (2016). Statistical tests, p values, confidence intervals, and power: A guide to misinterpretations. European Journal of Epidemiology, 31(4), 337–50. http://doi.org/10.1007/s10654-016-0149-3 - -* Lakens, D. (2013). Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs. Frontiers in Psychology, 4, 863. 10.3389/fpsyg.2013.00863 - -* Pek, J., & Flora, D. B. (2018). Reporting effect sizes in original psychological research: A discussion and tutorial. Psychological Methods, 23(2), 208-225. http://doi.org/10.1037/met0000126 - -* Perugini, M., Gallucci, M., & Costantini, G. (2014). Safeguard power as a protection against imprecise power estimates. Perspectives on Psychological Science, 9, 319-332. - -
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- -## Research Design, Sample Methods, and its implications for inferences. - -* Gervais et al. (2015). A powerful nudge? Presenting calculable consequences of underpowered research shifts incentives towards adequately powered designs. Social Psychological and Personality Science, 6, 847-854. https://doi.org/10.1177/1948550615584199 - -* Perugini, M., Gallucci, M., & Costantini, G. (2014). Safeguard power as a protection against imprecise power estimates. Perspectives on Psychological Science, 9, 319-332. - -* Wicherts, J. M., Veldkamp, C. L., Augusteijn, H. E., Bakker, M., Van Aert, R., & Van Assen, M. A. (2016). Degrees of freedom in planning, running, analyzing, and reporting psychological studies: A checklist to avoid p-hacking. Frontiers in Psychology, 7, 1832.doi: 10.3389/fpsyg.2016.01832 - -
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- -## Questionable measurement practices (QMPs), validity and reliability issues. - -* Flake, J. K., & Fried, E. I. (2019, January 17). Measurement schmeasurement: Questionable measurement practices and how to avoid them. https://doi.org/10.31234/osf.io/hs7wm - -* Flake, J. K., Pek, J., & Hehman, E. (2017). Construct validation in social and personality research: Current practice and recommendations. Social Psychological and Personality Science, 8(4), 370–378. https://doi.org/10.1177/1948550617693063 - -* Hussey, I., & Hughes, S. (2018, November 19). Hidden invalidity among fifteen commonly used measures in social and personality psychology. https://doi.org/10.31234/osf.io/7rbfp - -* Rodebaugh, T. L., Scullin, R. B., Langer, J. K., Dixon, D. J., Huppert, J. D., Bernstein, A., . . . Lenze, E. J. (2016). Unreliability as a threat to understanding psychopathology: The cautionary tale of attentional bias. Journal of Abnormal Psychology, 125(6), 840-851. http://dx.doi.org/10.1037/abn0000184 - -
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\ No newline at end of file diff --git a/content/clusters/cluster3.md b/content/clusters/cluster3.md deleted file mode 100644 index 9412065d520..00000000000 --- a/content/clusters/cluster3.md +++ /dev/null @@ -1,176 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 10 # Order that this section will appear. - -title = "Cluster 3: Reproducible analyses" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "red" - color = "#DAD5DD" - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1rem;" - - # CSS class. - css_class = "" -+++ - -### Description - -Attainment of the *how-to* basics of reproducible reports and analyses. It requires students to move towards transparent and scripted analysis practices. There are 6 sub-clusters which aim to further parse the learning and teaching process: - -* Strengths of reproducible pipelines. -* Scripted analyses compared with GUI. -* Data wrangling. -* Programming reproducible data analyses. -* Open source and free software. -* Tools to check yourself and others. - -
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- -## Strengths of reproducible pipelines. - -***Automating data analysis to make the process easier*** - -* Gandrud, C. (2016). Reproducible research with R and R Sstudio. New York; CRC Press - -* Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, et al. (2017) Good enough practices in scientific computing. PLOS Computational Biology 13(6): e1005510. https://doi.org/10.1371/journal.pcbi.1005510 - -* [Reproducible Research in R Workshop Overview](https://datacarpentry.org/rr-workshop/) - -* [Monash's](https://github.com/MonashDataFluency) Data Fluency [Reproducible Research in R (RRR)](https://monashdatafluency.github.io/r-rep-res/index.html) - -* [ProjectTier](https://www.projecttier.org) - -
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- -## Scripted analyses compared with GUI. - -***Writing analyses in programming language compared to performing them with a point-and-click menu.*** - -* Gandrud, C. (2016). Reproducible research with R and R Sstudio. New York; CRC Press - -
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- -## Data wrangling - -***Processing and restructuring data so that it is more useful for analyse.*** - -Nick Fox's [Writing Reproducible Scientific Papers in R](https://www.youtube.com/playlist?list=PLmvNihjFsoM5hpQdqoI7onL4oXDSQ0ym8) - -PsuTeachR's [Data Skills for Reproducible Science](https://psyteachr.github.io/msc-data-skills/) - -
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- -## Programming reproducible data analyses - -***Making sure anyone can reproduce analyses through things like well-commented scripts, writing codebooks, etc.*** - -* Gandrud, C. (2016). Reproducible research with R and R Sstudio. New York; CRC Press - -* Wilson, G., Bryan, J., Cranston, K., Kitzes, J., Nederbragt, L., & Teal, T. K. (2017). Good enough practices in scientific computing. PLoS computational biology, 13(6). e1005510. https://doi.org/10.1371/journal.pcbi.1005510 - -* [Open Stats Lab](https://sites.trinity.edu/osl/) - -* [Software Carpentry](https://software-carpentry.org/) - -* [Learning statistics with R: A tutorial for psychology students and other beginners](https://learningstatisticswithr.com/book/) - -
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- -## Open source and free software. - -* Chao, L. (2009). Utilizing open source tools for online teaching and learning Information Science. Hershey, PA: Information Science Reference. - -
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- -## Tools to check yourself and others - -***Includes tools such as statcheck.io, GRIM, and SPRITE*** - -* Brown, N. J., & Heathers, J. A. (2016). The GRIM test: A simple technique detects numerous anomalies in the reporting of results in psychology. Social Psychological and Personality Science, 1948550616673876. https://doi.org/10.1177/1948550616673876 - -* Nuijten, M. B., Van Assen, M. A. L. M., Hartgerink, C. H. J., Epskamp, S., & Wicherts, J. M. (2017). The validity of the tool “statcheck” in discovering statistical reporting inconsistencies. Preprint retrieved from https://psyarxiv.com/tcxaj/. - -* van der Zee, T., Anaya, J., & Brown, N. J. (2017). Statistical heartburn: An attempt to digest four pizza publications from the Cornell Food and Brand Lab. BMC Nutrition, 3(1), 54. DOI 10.1186/s40795-017-0167-x - - -
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diff --git a/content/clusters/cluster4.md b/content/clusters/cluster4.md deleted file mode 100644 index 3d351c07d30..00000000000 --- a/content/clusters/cluster4.md +++ /dev/null @@ -1,212 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 10 # Order that this section will appear. - -title = "Cluster 4: Open (FAIR) data and materials analyses" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "red" - color = "#BDC5CA" - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1rem;" - - # CSS class. - css_class = "" -+++ - -### Description - -Attainment of a grounding in open (FAIR) data and materials. It requires students to learn about FAIR data (and education materials) principles: findability, accessibility, interoperability, and reusability; engage with reasons to share data, the initiatives designed to increase scientific openness; as well as ethical considerations and consequences of open (FAIR) data practices. There are 6 sub-clusters which aim to further parse the learning and teaching process: - -* Publication models. -* Reasons to share; for science, and for one’s own practices. -* Repositories such as OSF, FigShare, GitHub, Zenodo. -* Accessing or sharing others data, code, and materials. -* Ethical considerations. -* Examples and consequences of accessing un/open data. - -
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- -## Publication models - -***Traditional publication models, open access models, preprints, etc.*** - -* Hardwicke, T. E., Mathur, M. B., MacDonald, K., Nilsonne, G., Banks, G. C., Kidwell, M. C., ... & Lenne, R. L. (2018). Data availability, reusability, and analytic reproducibility: Evaluating the impact of a mandatory open data policy at the journal Cognition. Royal Society Open Science, 5(8), 180448. http://dx.doi.org/10.1098/rsos.180448 - -* Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., … Nosek, B. A. (2018). Many Labs 2: Investigating Variation in Replicability Across Samples and Settings. Advances in Methods and Practices in Psychological Science, 1(4), 443–490. https://doi.org/10.1177/2515245918810225 - -* Klein, R. A., Ratliff, K. A., Vianello, M., Adams, R. B., Bahník, Š., Bernstein, M. J., et al. (2014). Investigating variation in replicability: A “many labs” replication project. Social Psychology, 45, 142–152. https://doi.org/10.1027/1864-9335/a000178 - -* Rouder, J. N. (2016). The what, why, and how of born open data. Behavior Research Methods, 48, 1062–1069. doi:10.3758/s13428-015-0630-z - -* Siler, K., Haustein, S., Smith, E., Larivière, V., & Alperin, J. P. (2018). Authorial and institutional stratification in open access publishing: the case of global health research. PeerJ, 6, e4269. doi:10.7717/peerj.4269 - -* Tennant, J. P., Waldner, F., Jacques, D. C., Masuzzo, P., Collister, L. B., & Hartgerink, C. H. (2016). The academic, economic and societal impacts of Open Access: an evidence-based review. F1000Research, 5, 632. doi:10.12688/f1000research.8460.3 - - -
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- -## Reasons to share; for science, and for one’s own practices - -* Colavizza, G., Hrynaszkiewicz, I., Staden, I., Whitaker, K., & McGillivray, B. (2020). The citation advantage of linking publications to research data. PloS One, 15(4), e0230416. - -* Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., … Nosek, B. A. (2018). Many Labs 2: Investigating Variation in Replicability Across Samples and Settings. Advances in Methods and Practices in Psychological Science, 1(4), 443–490. https://doi.org/10.1177/2515245918810225 - -* Klein, R. A., Ratliff, K. A., Vianello, M., Adams, R. B., Bahník, Š., Bernstein, M. J., et al. (2014). Investigating variation in replicability: A “many labs” replication project. Social Psychology, 45, 142–152. https://doi.org/10.1027/1864-9335/a000178 - -* Levenstein, M. C., & Lyle, J. A. (2018). Data: Sharing Is Caring. Advances in Methods and Practices in Psychological Science, 1(1), 95–103. https://doi.org/10.1177/2515245918758319 - -* Piwowar, H.A., & Vision, T.J. (2013). Data reuse and the open data citation advantage. PeerJ, 1, e175 https://doi.org/10.7717/peerj.175 - -* Rouder, J. N. (2016). The what, why, and how of born open data. Behavior Research Methods, 48, 1062–1069. doi:10.3758/s13428-015-0630-z - -* Stodden, V. C. (2011). Trust your science? Open your data and code. Amstat News, 409, 21-22. - -* Tennant, J. P., Waldner, F., Jacques, D. C., Masuzzo, P., Collister, L. B., & Hartgerink, C. H. (2016). The academic, economic and societal impacts of Open Access: an evidence-based review. F1000Research, 5, 632. doi:10.12688/f1000research.8460.3 - -
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- -## Repositories such as OSF, FigShare, GitHub, Zenodo - -* Gilmore, R. O., Kennedy, J. L., & Adolph, K. E. (2018). Practical solutions for sharing data and materials from psychological research. Advances in Methods and Practices in Psychological Science, 1(1), 121–130. https://doi.org/10.1177/2515245917746500 - -* Rouder, J. N. (2016). The what, why, and how of born open data. Behavior Research Methods, 48, 1062–1069. doi:10.3758/s13428-015-0630-z - -* Soderberg, C. K. (2018). Using OSF to Share Data: A Step-by-Step Guide. Advances in Methods and Practices in Psychological Science, 1(1), 115–120. https://doi.org/10.1177/2515245918757689 - -* [osf.io](https://osf.io) - -* [figshare.com](https://figshare.com) - -* [github.com](https://github.com) - -* [zenodo.org](https://zenodo.org/) - -
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- -## Accessing or sharing others data, code, and materials - -* Joel, S., Eastwick, P. W., & Finkel, E. J. (2018). Open sharing of data on close relationships and other sensitive social psychological topics: Challenges, tools, and future directions. Advances in Methods and Practices in Psychological Science, 1(1), 86–94. https://doi.org/10.1177/2515245917744281 - -* Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., … Nosek, B. A. (2018). Many Labs 2: Investigating Variation in Replicability Across Samples and Settings. Advances in Methods and Practices in Psychological Science, 1(4), 443–490. https://doi.org/10.1177/2515245918810225 - -* Klein, R. A., Ratliff, K. A., Vianello, M., Adams, R. B., Bahník, Š., Bernstein, M. J., et al. (2014). Investigating variation in replicability: A “many labs” replication project. Social Psychology, 45, 142–152. https://doi.org/10.1027/1864-9335/a000178 - -* Piwowar, H.A., & Vision, T.J. (2013). Data reuse and the open data citation advantage. PeerJ, 1, e175 https://doi.org/10.7717/peerj.175 - -* Wicherts, J. M., Borsboom, D., Kats, J., & Molenaar, D. (2006). The poor availability of psychological research data for reanalysis. American Psychologist, 61(7), 726–728. https://doi.org/10.1037/0003-066X.61.7.726 - -* Wicherts, J. M., Veldkamp, C. L., Augusteijn, H. E., Bakker, M., Van Aert, R., & Van Assen, M. A. (2016). Degrees of freedom in planning, running, analyzing, and reporting psychological studies: A checklist to avoid p-hacking. Frontiers in Psychology, 7, 1832. - -
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- -## Ethical considerations - -* Hand, D. J. (2018). Aspects of data ethics in a changing world: Where are we now? Big Data, 6(3), :176–190. doi: https://doi.org/10.1089/big.2018.0083 - -* O’Callaghan, E., & Douglas, H. M. (2021). #MeToo Online Disclosures: A Survivor-Informed Approach to Open Science Practices and Ethical Use of Social Media Data. Psychology of Women Quarterly, 45(4), 505–525. https://doi.org/10.1177/03616843211039175 - -* Ross, M. W., Iguchi, M. Y., & Panicker, S. (2018). Ethical aspects of data sharing and research participant protections. American Psychologist, 73(2), 138-145. http://dx.doi.org/10.1037/amp0000240 - -* Siler, K., Haustein, S., Smith, E., Larivière, V., & Alperin, J. P. (2018). Authorial and institutional stratification in open access publishing: the case of global health research. PeerJ, 6, e4269. doi:10.7717/peerj.4269 - -* Walsh, C. G., Xia, W., Li, M., Denny, J. C., Harris, P. A., & Malin, B. A. (2018). Enabling open-science initiatives in clinical psychology and psychiatry without sacrificing patients’ privacy: Current practices and future challenges. Advances in Methods and Practices in Psychological Science, 1(1), 104–114. https://doi.org/10.1177/2515245917749652 - -
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- -## Examples and consequences of accessing un/open data - -* Houtkoop, B. L., Chambers, C., Macleod, M., Bishop, D. V. M., Nichols, T. E., & Wagenmakers, E.-J. (2018). Data sharing in psychology: A survey on barriers and preconditions. Advances in Methods and Practices in Psychological Science, 1(1), 70–85. https://doi.org/10.1177/2515245917751886 - -* Peng, R. (2015). The reproducibility crisis in science: A statistical counterattack. Significance, 12(3). https://doi.org/10.1111/j.1740-9713.2015.00827.x - -* Rouder, J. N. (2016). The what, why, and how of born open data. Behavior Research Methods, 48, 1062–1069. doi:10.3758/s13428-015-0630-z - -* Walsh, C. G., Xia, W., Li, M., Denny, J. C., Harris, P. A., & Malin, B. A. (2018). Enabling open-science initiatives in clinical psychology and psychiatry without sacrificing patients’ privacy: Current practices and future challenges. Advances in Methods and Practices in Psychological Science, 1(1), 104–114. https://doi.org/10.1177/2515245917749652 - -* Wicherts, J. M., Borsboom, D., Kats, J., & Molenaar, D. (2006). The poor availability of psychological research data for reanalysis. American Psychologist, 61(7), 726–728. https://doi.org/10.1037/0003-066X.61.7.726 - -* Wicherts, J. M., Veldkamp, C. L., Augusteijn, H. E., Bakker, M., Van Aert, R., & Van Assen, M. A. (2016). Degrees of freedom in planning, running, analyzing, and reporting psychological studies: A checklist to avoid p-hacking. Frontiers in Psychology, 7, 1832. - - - -
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diff --git a/content/clusters/cluster5.md b/content/clusters/cluster5.md deleted file mode 100644 index 08613f0bdca..00000000000 --- a/content/clusters/cluster5.md +++ /dev/null @@ -1,183 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 10 # Order that this section will appear. - -title = "Cluster 5: Preregistration" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "red" - # color = "#C4DCE1" - color = "#b6cac8" - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1rem;" - - # CSS class. - css_class = "" -+++ - -### Description - -Preregistration entails laying out a complete methodology and analysis before a study has been undertaken. This facilitates transparency and removes several potential QRPs. When teaching, students should attain knowledge regarding what a pre-registration entails, why it is important to remove potential QRPs and how to address deviations from preregistered plans. -There are 6 sub-clusters which aim to further parse the learning and teaching process: - -* Purpose of preregistration. -* Preregistration and registered reports - strengths and differences. -* When can you preregister? Can you pre-register secondary data? -* Understanding the types of preregistration and writing one. -* Comparing a preregistration to a final study manuscript. -* Conducting a preregistered study. - -
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- -## Purpose of preregistration - -***Distinguishing exploratory and confirmatory analyses, transparency measures.*** - -* Dal-Ré, R., Ioannidis, J. P., Bracken, M. B., Buffler, P. A., Chan, A.-W., Franco, E. L., La Vecchia, C., Weiderpass, E. (2014). Making prospective registration of observational research a reality. Science translational medicine, 6(224), 224cm1. DOI: https://doi.org/10.1126/scitranslmed.3007513 - -* Nosek, B. A., & Lakens, D. (2014). Registered reports: A method to increase the credibility of published results. Social Psychology, 45, 137–141. - -* Lin, W., & Green, D. P. (2016). Standard operating procedures: A safety net for pre-analysis plans. PS: Political Science & Politics, 49(3), 495-500. - -* Nosek, B. A., Ebersole, C. R., DeHaven, A., & Mellor, D. (2018). The Preregistration Revolution. Proceedings of National Academy Sciences, 115(11), 2600-2606. https://doi.org/10.1073/pnas.1708274114 - -* Wicherts, J. M., Veldkamp, C. L., Augusteijn, H. E., Bakker, M., Van Aert, R., & Van Assen, M. A. (2016). Degrees of freedom in planning, running, analyzing, and reporting psychological studies: A checklist to avoid p-hacking. Frontiers in Psychology, 7, 1832.doi: 10.3389/fpsyg.2016.01832 - -* Nuzzo, R. (2015). How scientists fool themselves — and how they can stop. Nature, 526, 182–185. - -* Wagenmakers, E. J., & Dutilh, G. (2016). Seven selfish reasons for preregistration. APS Observer, 29(9). - -
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- -## Preregistration and registered reports - strengths and differences - -***OSC, CREP, ManyLabs, etc.** - -* Chambers, C. D. (2013). Registered reports: A new publishing initiative at Cortex. Cortex, 49(3), 609-610. https://doi.org/10.1016/j.cortex.2012.12.016 - -* Chambers, C. D., Feredoes, E., Muthukumaraswamy, S. D., & Etchells, P. (2014). Instead of “playing the game” it is time to change the rules: Registered Reports at AIMS Neuroscience and beyond. AIMS Neuroscience, 1(1), 4–17. DOI: 10.3934/Neuroscience2014.1.4 - -* Chambers, C.D., Dienes, Z., McIntosh, R.D., Rotshtein, P., & Willmes, K. (2015). Registered Reports: Realigning incentives in scientific publishing. Cortex, 66, A1-2. DOI: 10.1016/j.cortex.2015.03.022 - -
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- -## When can you preregister? Can you pre-register secondary data? - -* Chambers, C.D., Dienes, Z., McIntosh, R.D., Rotshtein, P., & Willmes, K. (2015). Registered Reports: Realigning incentives in scientific publishing. Cortex, 66, A1-2. DOI: https://doi.org/10.1016/j.cortex.2015.03.022 - -* Haven, Tamarinde., L. & Van Grootel, Leonie. (2019). Preregistering qualitative research. Accountability in Research, 26(3), 229-244., DOI: https://doi.org/10.1080/08989621.2019.1580147 - -* Kirtley, O. J., Lafit, G., Achterhof, R., Hiekkaranta, A. P., & Myin-Germeys, I. (2019, April 10). Making the black box transparent: A pre-registration template for studies using Experience Sampling Methods (ESM). https://doi.org/10.31234/osf.io/seyq7 - -* Mertens, G., & Krypotos, A. (2019, February 20). Preregistration of secondary analyses. https://doi.org/10.31234/osf.io/ph4q7 - -
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- -## Understanding the types of preregistration and writing one. - -* Nosek, B. A., Ebersole, C. R., DeHaven, A. C., & Mellor, D. T. (2018). The preregistration revolution. Proceedings of the National Academy of Sciences, 115(11), 2600-2606. https://doi.org/10.1073/pnas.1708274114 - -* Mertens, G., & Krypotos, A. (2019, February 20). Preregistration of secondary analyses. https://doi.org/10.31234/osf.io/ph4q7 - -* COS: [What is Preregistration?](https://cos.io/prereg/) - -* COS: [10 Tips for Making a Great Preregistration](https://cos.io/blog/10-preregistration-tips/) - -* COS: [8 Answers About Registered Reports and Research Preregistration](https://www.wiley.com/network/researchers/being-a-peer-reviewer/registered-reports-good-for-both-science-and-authors) - -
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- -## Comparing a preregistration to a final study manuscript. - -* [Wiley's Reviewing Registered Reports](https://authorservices.wiley.com/Reviewers/journal-reviewers/how-to-perform-a-peer-review/reviewing-registered-reports.html) - -
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- -## Conducting a preregistered study. - -* L. Haven, T., & Van Grootel, D. L. (2019). Preregistering qualitative research. Accountability in Research, 26(3), 229-244. https://doi.org/10.1080/08989621.2019.1580147 - -* Nosek, B. A., Ebersole, C. R., DeHaven, A., & Mellor, D. (2018). The Preregistration Revolution. PNAS, 115(11), 2600-2606. https://doi.org/10.1073/pnas.1708274114 - -* COS: [One Preregistration to Rule Them All?](https://www.cos.io/blog/one-preregistration-rule-them-all) - -
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diff --git a/content/clusters/cluster6.md b/content/clusters/cluster6.md deleted file mode 100644 index 9af37db12ae..00000000000 --- a/content/clusters/cluster6.md +++ /dev/null @@ -1,201 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 10 # Order that this section will appear. - -title = "Cluster 6: Replication research" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "red" - # color = "#d4bbaa" - # color = "#d4bbaa" - color = "#bacabd" - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1rem;" - - # CSS class. - css_class = "" -+++ - -### Description - -Attainment of a grounding in 'replication research', which takes a variety of forms, each with a different purpose and contribution. Reproducible science requires replication research. When teaching, students should understand the purpose and need of replications in its variety of forms and being able to conduct (and join) replication projects. There are 6 sub-clusters which aim to further parse the learning and teaching process: - -* Purposes of replication attempts - what is a ‘failed’ replication? -* Large scale replication attempts. -* Distinguishing direct and conceptual replications. -* Conducting replication studies; challenges, limitations, and comparisons with the original study. -* Registered Replication Reports (RRR). -* The politics of replicating famous studies. - -
- - - -
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- -## Purposes of replication attempts - what is a ‘failed’ replication? - -* Fidler, F., & Wilcox, J. (2018). Reproducibility of scientific results. In E. N. Zalta (Ed.), The Stanford encyclopedia of philosophy (Winter 2018). Metaphysics Research Lab, Stanford University. https://plato.stanford.edu/archives/win2018/entries/scientific-reproducibility/ - -* Frank, M. C., & Saxe, R. (2012). Teaching replication. Perspectives on Psychological Science, 7(6), 600–604. https://doi.org/10.1177/1745691612460686 - -* García, FM. (2016). Replication and the manufacture of scientific inferences: A formal approach. International Studies Perspectives, 17(4), 408–425. https://doi.org/10.1093/isp/ekv011 - -* Van Bavel, J. J., Mende-Siedlecki, P., Brady, W. J., & Reinero, D. A. (2016). Contextual sensitivity in scientific reproducibility. Proceedings of the National Academy of Sciences, 113(23), 6454-6459. https://doi.org/10.1073/pnas.1521897113 - -* Zwaan, R.A., Etz, A., Lucas, R.E, Donnellan, M.B. (2018). Making replication mainstream. Behavior and Brain Sciences, 41, e120. https://doi.org/10.1017/S0140525X17001972 - -
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- -## Large scale replication attempts - -***OSC, CREP, ManyLabs, etc.** - -* Klein, R. A., Ratliff, K. A., Vianello, M., Adams, R. B., Bahník, Š., Bernstein, M. J., et al. (2014). Investigating variation in replicability: A “many labs” replication project. Social Psychology, 45, 142–152. https://doi.org/10.1027/1864-9335/a000178 - -* Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., … Nosek, B. A. (2018). Many Labs 2: Investigating Variation in Replicability Across Samples and Settings. Advances in Methods and Practices in Psychological Science, 1(4), 443–490. https://doi.org/10.1177/2515245918810225 - -* Open Science Collaboration (2012). An open, large-scale, collaborative effort to estimate the reproducibility of psychological science. Perspectives on Psychological Science, 7, 657–660. - -* Open Science Collaboration. (2015). Estimating the reproducibility of psychological science. Science, 349(6251), aaC6716. DOI: 10.1126/science.aaC6716 - -* Van Bavel, J. J., Mende-Siedlecki, P., Brady, W. J., & Reinero, D. A. (2016). Contextual sensitivity in scientific reproducibility. Proceedings of the National Academy of Sciences, 113(23), 6454-6459. https://doi.org/10.1073/pnas.1521897113 - -* [ManyPrimates](https://manyprimates.github.io/) - -* [CREP](https://osf.io/wfc6u/) - -
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- -## Distinguishing direct and conceptual replications - -***Direct replications use the exact same methods and materials, while conceptual replications test the same concept but with different methods, materials, or both.*** - -* Kunert, R. (2016). Internal conceptual replications do not increase independent replication success. Psychonomic bulletin & review, 23(5), 1631-1638. https://doi.org/10.3758/s13423-016-1030-9 - -* Simons, D. J. (2014). The Value of Direct Replication. Perspectives on Psychological Science, 9(1), 76–80. https://doi.org/10.1177/1745691613514755 - -* Van Bavel, J. J., Mende-Siedlecki, P., Brady, W. J., & Reinero, D. A. (2016). Contextual sensitivity in scientific reproducibility. Proceedings of the National Academy of Sciences, 113(23), 6454-6459. https://doi.org/10.1073/pnas.1521897113 - -* Zwaan, R.A., Etz, A., Lucas, R.E, Donnellan, M.B. (2018). Making replication mainstream. Behavior and Brain Sciences, 41, e120. https://doi.org/10.1017/S0140525X17001972 - - -
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- -## Conducting replication studies; challenges, limitations, and comparisons with the original study - -* Grahe, J. E., Brandt, M. J., Wagge, J. R., Legate, N., Wiggins, B. J., Christopherson, C. D., . . . LePine, S. (2018). Collaborative Replications and Education Project (CREP). Retrieved from https://osf.io/wfc6u/ - -* Grahe, J. E., Reifman, A., Hermann, A. D., Walker, M., Oleson, K. C., Nario-Redmond, M., & Wiebe, R. P. (2012). Harnessing the undiscovered resource of student research projects. Perspectives on Psychological Science, 7(6), 605–607. https://doi.org/10.1177/1745691612459057 - -* Frank, M. C., & Saxe, R. (2012). Teaching replication. Perspectives on Psychological Science, 7(6), 600–604. https://doi.org/10.1177/1745691612460686 - -* Lenne & Mann (2016). CREP project report. https://osf.io/sdj7e/ - -* Stanley, D. J., & Spence, J. R. (2014). Expectations for replications: Are yours realistic? Perspectives on Psychological Science, 9(3), 305-318. https://doi.org/10.1177/1745691614528518 - -* Wagge, J. R., Brandt, M. J., Lazarevic, L. B., Legate, N., Christopherson, C., Wiggins, B., & Grahe, J. E. (2019). Publishing research with undergraduate students via replication work: The collaborative replications and education project. Frontiers in psychology, 10, 247. - - -
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- -## Registered Replication Reports - -***Registered Reports are studies that are peer-reviewed prior to data collection, with an agreement between the journal and the author(s) that it will be published regardless of outcome as long as the preregistered methods are reasonably followed. Registered REPLICATION Reports are a special category of these that only include replications.*** - -* Simons, D. J., Holcombe, A. O., & Spellman, B. A. (2014). An Introduction to Registered Replication Reports at Perspectives on Psychological Science. Perspectives on Psychological Science, 9(5), 552–555. https://doi.org/10.1177/1745691614543974 - -* Ongoing Replication projects https://www.psychologicalscience.org/publications/replication/ongoing-projects - -* Alogna, V. K., Attaya, M. K., Aucoin, P., Bahník, Š., Birch, S., Birt, A. R., ... & Buswell, K. (2014). Registered replication report: Schooler and engstler-schooler (1990). Perspectives on Psychological Science, 9(5), 556-578. - -* Eerland, A., Sherrill, A. M., Magliano, J. P., Zwaan, R. A., Arnal, J. D., Aucoin, P., ... & Crocker, C. (2016). Registered replication report: Hart & albarracín (2011). Perspectives on Psychological Science, 11(1), 158-171. - -[Psychological Science Accelerator (PSA) Ongoing Replications](https://www.psychologicalscience.org/publications/replication/ongoing-projects) - - -
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- -## The politics of replicating famous studies - -***Sometimes responses to replication research can be negative. Failed replications of famous work, most notably power posing, ego depletion, stereotype threat, and facial feedback, have received a lot of attention.*** - -* Neuliep, J. W., & Crandall, R. (1990). Editorial bias against replication research. Journal of Social Behavior & Personality, 5(4), 85-90. - -* Neuliep, J. W., & Crandall, R. (1993). Reviewer bias against replication research. Journal of Social Behavior & Personality, 8(6), 21-29. - -
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diff --git a/content/clusters/cluster7.md b/content/clusters/cluster7.md deleted file mode 100644 index 8d179217df3..00000000000 --- a/content/clusters/cluster7.md +++ /dev/null @@ -1,359 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = false # Activate this widget? true/false -weight = 10 # Order that this section will appear. - -title = "Cluster 7: Academic Life, Ethics and Culture" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "red" - # color = "#F4CE5B" - # color = "#F6D87C" - color = "#c9dbcb" - # Background gradient. - #gradient_start = "#d4bbaa" - #gradient_end = "#88664c" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1rem;" - - # CSS class. - css_class = "" -+++ - -### Description - -Attainment of a grounding in topics related to academia and academics. Students should understand how individuals, teams, institutions, and academic culture work together to promote (or hinder) openness, inclusion, diversity, equity and transparency. Gathering perspectives on navigating scientific and academic life. Learning the challenges and rewards in the academic setting, the “hidden curriculum” in academic life. - - - -There are 8 sub-clusters which aim to further parse the learning and teaching process: - -* Diversity -* Equity -* Inclusion -* Citizen science -* Team science -* Adversarial collaboration -* The structure of and incentives in academia -* Types of academic, non-academic & alt-academic positions - -
- - - -
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- -## Diversity - -***Diversity is the presence of difference within a specific environment, e.g. racial diversity, gender diversity, social-economic diversity, etc.*** - -* Bahlai, C., Bartlett, L. J., Burgio, K. R., Fournier, A., Keiser, C. N., Poisot, T., & Whitney, K. S. (2019). Open science isn’t always open to all scientists. American Scientist, 107(2), 78-82. https://doi.org/10.1511/2019.107.2.78 - -* Cislak, A., Formanowicz, M., & Saguy, T. (2018). Bias against research on gender bias. Scientometrics, 115(1), 189-200. https://doi.org/10.1007/s11192-018-2667-0 - -* Flaherty, C. (2020, August, 20). Something's Got to Give. Inside Higher Ed. Retrieved from https://www.insidehighered.com/news/2020/08/20/womens-journal-submission-rates-continue-fall - -* Kim, E., & Patterson, S. (2020). The Pandemic and Gender Inequality in Academia. Available at SSRN 3666587. http://dx.doi.org/10.2139/ssrn.3666587 - -* Larivière, V., Ni, C., Gingras, Y., Cronin, B., & Sugimoto, C. R. (2013). Bibliometrics: Global gender disparities in science. Nature News, 504(7479), 211. https://doi.org/10.1038/504211a - -* Myers, K. R., Tham, W. Y., Yin, Y., Cohodes, N., Thursby, J. G., Thursby, M. C., ... & Wang, D. (2020). Unequal effects of the COVID-19 pandemic on scientists. Nature human behaviour, 4(9), 880-883. - -* Quagliata, T. (2008). Is there a positive correlation between socioeconomic status and academic achievement?. Paper: Education masters (p. 78). https://fisherpub.sjfc.edu/cgi/viewcontent.cgi?article=1077&context=education_ETD_masters - -* Roberson, M. L. (2020). On supporting early-career Black scholars. Nature Human Behaviour, 1-1. https://doi.org/10.1038/s41562-020-0926-6 - -* APA (2010). Sexual Orientation, Gender identity & Socioeconomic Status [Blog post]. Retrieved fromhttps://www.apa.org/pi/ses/resources/publications/lgbt - -* APA (2010). Disability & Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/disability - -* APA. (2017, July). Women & Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/women - -* APA (2017, July). Ethnic and Racial Minorities & Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/minorities - -* APA (2017, July). Education and Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/education - -
-
-

- -***Equity is that everyone has access to the same opportunities and that we all have privileges and barriers, thus we do not all start from the same starting position.*** - -* APA (2010). Sexual Orientation, Gender identity & Socioeconomic Status [Blog post]. Retrieved fromhttps://www.apa.org/pi/ses/resources/publications/lgbt - -* APA (2010). Disability & Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/disability - -* APA. (2017, July). Women & Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/women -APA (2017, July). Ethnic and Racial Minorities & Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/minorities - -* APA (2017, July). Education and Socioeconomic Status [Blog post]. Retrieved from https://www.apa.org/pi/ses/resources/publications/education - -* Bahlai, C., Bartlett, L. J., Burgio, K. R., Fournier, A., Keiser, C. N., Poisot, T., & Whitney, K. S. (2019). Open science isn’t always open to all scientists. American Scientist, 107(2), 78-82. https://doi.org/10.1511/2019.107.2.78 - -* Cislak, A., Formanowicz, M., & Saguy, T. (2018). Bias against research on gender bias. Scientometrics, 115(1), 189-200. https://doi.org/10.1007/s11192-018-2667-0 - -* Flaherty, C. (2020, August, 20). Something's Got to Give. Inside Higher Ed. Retrieved from https://www.insidehighered.com/news/2020/08/20/womens-journal-submission-rates-continue-fall - -* Kim, E., & Patterson, S. (2020). The Pandemic and Gender Inequality in Academia. Available at SSRN 3666587. http://dx.doi.org/10.2139/ssrn.3666587 - -* Larivière, V., Ni, C., Gingras, Y., Cronin, B., & Sugimoto, C. R. (2013). Bibliometrics: Global gender disparities in science. Nature News, 504(7479), 211. https://doi.org/10.1038/504211a - -* Myers, K. R., Tham, W. Y., Yin, Y., Cohodes, N., Thursby, J. G., Thursby, M. C., ... & Wang, D. (2020). Unequal effects of the COVID-19 pandemic on scientists. Nature human behaviour, 4(9), 880-883. - -* Quagliata, T. (2008). Is there a positive correlation between socioeconomic status and academic achievement?. Paper: Education masters (p. 78). https://fisherpub.sjfc.edu/cgi/viewcontent.cgi?article=1077&context=education_ETD_masters - -* Roberson, M. L. (2020). On supporting early-career Black scholars. Nature Human Behaviour, 1-1. https://doi.org/10.1038/s41562-020-0926-6 - -
-
-

- -## Inclusion - -***Inclusion is that individuals with different representations, identities and feelings being respected, influenced, and welcomed in a specific environment.*** - -* Bahlai, C., Bartlett, L. J., Burgio, K. R., Fournier, A., Keiser, C. N., Poisot, T., & Whitney, K. S. (2019). Open science isn’t always open to all scientists. American Scientist, 107(2), 78-82. https://doi.org/10.1511/2019.107.2.78 - -* Carli, L. L., Alawa, L., Lee, Y., Zhao, B., & Kim, E. (2016). Stereotypes about gender and science: Women≠ scientists. Psychology of Women Quarterly, 40(2), 244-260 https://doi.org/10.1177/0361684315622645 - -* Cislak, A., Formanowicz, M., & Saguy, T. (2018). Bias against research on gender bias. Scientometrics, 115(1), 189-200. https://doi.org/10.1007/s11192-018-2667-0 - -* Eagly, A. H., & Miller, D. I. (2016). Scientific eminence: Where are the women?. Perspectives on Psychological Science, 11(6), 899-904. - -* Flaherty, C. (2020, August, 20). Something's Got to Give. Inside Higher Ed. Retrieved from https://www.insidehighered.com/news/2020/08/20/womens-journal-submission-rates-continue-fall - -* Henrich, J., Heine, S. & Norenzayan, A. (2010) Most people are not WEIRD. Nature 466, 29. https://doi.org/10.1038/466029a - -* Larivière, V., Ni, C., Gingras, Y., Cronin, B., & Sugimoto, C. R. (2013). Bibliometrics: Global gender disparities in science. Nature News, 504(7479), 211. https://doi.org/10.1038/504211a - -* Macoun, A., & Miller, D. (2014). Surviving (thriving) in academia: Feminist support networks and women ECRs. Journal of Gender Studies, 23(3), 287-301. https://doi.org/10.1080/09589236.2014.909718 - -* Myers, K. R., Tham, W. Y., Yin, Y., Cohodes, N., Thursby, J. G., Thursby, M. C., ... & Wang, D. (2020). Unequal effects of the COVID-19 pandemic on scientists. Nature human behaviour, 4(9), 880-883. - -* Risner, L. E., Morin, X. K., Erenrich, E. S., Clifford, P. S., Franke, J., Hurley, I., & Schwartz, N. B. (2020). Leveraging a collaborative consortium model of mentee/mentor training to foster career progression of underrepresented postdoctoral researchers and promote institutional diversity and inclusion. PloS one, 15(9), e0238518. https://doi.org/10.1371/journal.pone.0238518 - -* Roberson, M. L. (2020). On supporting early-career Black scholars. Nature Human Behaviour, 1-1. https://doi.org/10.1038/s41562-020-0926-6 - -* Skitka, L. J., Melton, Z. J., Mueller, A. B., & Wei, K. Y. (2020). The Gender Gap: Who Is (and Is Not) Included on Graduate-Level Syllabi in Social/Personality Psychology. Personality and Social Psychology Bulletin, 0146167220947326. https://doi.org/10.1177/0146167220947326 - -
-
-

- -## Citizen science - -***Citizen science is scientific research conducted, in whole or in part, by amateur (or nonprofessional) scientists. Citizen science is sometimes described as "public participation in scientific research," participatory monitoring, and participatory action research whose outcomes are often advancements in scientific research by improving the scientific communities capacity, as well as an increasing the public's understanding of science.*** - -* Hart, D. D., & Silka, L. (2020). Rebuilding the ivory tower: bottom-up experiment in aligning research with societal needs. Issues Sci Technol, 36(3), 64-70. https://issues.org/aligning-research-with-societal-needs/ - -* Bonney, R., Cooper, C. B., Dickinson, J., Kelling, S., Phillips, T., Rosenberg, K. V., & Shirk, J. (2009). Citizen science: a developing tool for expanding science knowledge and scientific literacy. BioScience, 59(11), 977-984. - -* Bonney, R., Shirk, J. L., Phillips, T. B., Wiggins, A., Ballard, H. L., Miller-Rushing, A. J., & Parrish, J. K. (2014). Next steps for citizen science. Science, 343(6178), 1436-1437. - -* Cohn, J. P. (2008). Citizen science: Can volunteers do real research?. BioScience, 58(3), 192-197. - -
-
-

- -## Team science - -***Team science institutions coordinate a large group of scientists to solve a problem. Individual scientists are rewarded a publication by the institution for their efforts and resources. Once a group signs onto a team science project, the institution serves as a coordinating role, merging the resources from all scientists and focusing on a common project.*** - -* Forscher, P. S., Wagenmakers, E. J., DeBruine, L., Coles, N., Silan, M. A., & IJzerman, H. (2020). A Manifesto for Team Science. Retrieved from https://psyarxiv.com/2mdxh -Silberzahn, R., & Uhlmann, E. L. (2015). Crowdsourced research: Many hands make tight work. Nature News, 526(7572), 189. https://doi.org/10.1038/526189a - -* Wagge, J. R., Brandt, M. J., Lazarevic, L. B., Legate, N., Christopherson, C., Wiggins, B., & Grahe, J. E. (2019). Publishing research with undergraduate students via replication work: The collaborative replications and education project. Frontiers in psychology, 10, 247. https://doi.org/10.3389/fpsyg.2019.00247 - -
-
-

- -## Adversarial collaborations - - -* Tijdink, J. K., Verbeke, R., & Smulders, Y. M. (2014). Publication pressure and scientific misconduct in medical scientists. Journal of Empirical Research on Human Research Ethics, 9(5), 64-71. https://doi.org/10.1177/1556264614552421 - -* Bateman, I., Kahneman, D., Munro, A., Starmer, C., & Sugden, R. (2005). Testing competing models of loss aversion: An adversarial collaboration. Journal of Public Economics, 89(8), 1561-1580. - -
-
-

- -## Structures and Incentives in academia - -***Sometimes responses to replication research can be negative. Failed replications of famous work, most notably power posing, ego depletion, stereotype threat, and facial feedback, have received a lot of attention.*** - -* Bol, T., de Vaan, M., & van de Rijt, A. (2018). The Matthew effect in science funding. Proceedings of the National Academy of Sciences, 115(19), 4887-4890. - -* Corker, K. S. (2017). Why a Focus on Eminence is Misguided: A Call to Return to Basic Scientific Values. https://doi.org/10.31234/osf.io/yqfrd - -* Diener, E. (2016). Improving departments of psychology. Perspectives on Psychological Science, 11(6), 909-912. - -* Ebersole, C. R., Axt, J. R., & Nosek, B. A. (2016). Scientists’ reputations are based on getting it right, not being right. PLoS biology, 14(5), e1002460. - -* Fanelli, D. (2012). Negative results are disappearing from most disciplines and countries. Scientometrics, 90(3), 891-904. https://doi.org/10.1007/s11192-011-0494-7 - -* Feist, G. J. (2016). Intrinsic and extrinsic science: A dialectic of scientific fame. Perspectives on Psychological Science, 11(6), 893-898. - -* Ferreira, F. (2017). Fame: I’m Skeptical. https://doi.org/10.31234/osf.io/6zb4f - -* Flier J. (2017) Faculty promotion must assess reproducibility. Nature, 549(7671),133. https://doi.org/10.1038/549133a - -* Foss, D. J. (2016). Eminence and omniscience: Statistical and clinical prediction of merit. Perspectives on Psychological Science, 11(6), 913-916. - -* Gernsbacher, M. A. (2018). Rewarding research transparency. Trends in cognitive sciences, 22(11), 953-956. https://doi.org/10.1016/j.tics.2018.07.002 - -* Hirsch, J. E. (2010). An index to quantify an individual’s scientific research output that takes into account the effect of multiple coauthorship. Scientometrics, 85(3), 741-754. - -* Innes-Ker, Å. (2017). The Focus on Fame Distorts Science. https://doi.org/10.31234/osf.io/vyr3e - -* Ioannidis, J. P., & Thombs, B. D. (2019). A user’s guide to inflated and manipulated impact factors. European journal of clinical investigation, 49(9), e13151. https://doi.org/10.1111/eci.13151 - -* Jamieson, K. H., McNutt, M., Kiermer, V., & Sever, R. (2019). Signaling the trustworthiness of science. Proceedings of the National Academy of Sciences, 116(39), 19231-19236.https://doi.org/10.1073/pnas.1913039116 - -* Jamieson, K. H., McNutt, M., Kiermer, V., & Sever, R. (2020). Reply to Kornfeld and Titus: No distraction from misconduct. Proceedings of the National Academy of Sciences of the United States of America, 117(1), 42. https://doi.org/10.1073/pnas.1918001116 - -* Kornfeld, D. S., & Titus, S. L. (2016). Stop ignoring misconduct. Nature, 537(7618), 29-30.https://doi.org/10.1038/537029a - -* Kornfeld, D. S., & Titus, S. L. (2020). Signaling the trustworthiness of science should not be a substitute for direct action against research misconduct. Proceedings of the National Academy of Sciences of the United States of America, 117(1), 41. https://doi.org/10.1073/pnas.1917490116 - -* Li, W., Aste, T., Caccioli, F., & Livan, G. (2019). Early coauthorship with top scientists predicts success in academic careers. Nature communications, 10(1), 1-9. - -* Matosin, N., Frank, E., Engel, M., Lum, J. S., & Newell, K. A. (2014). Negativity towards negative results: a discussion of the disconnect between scientific worth and scientific culture. Disease Models & Mechanisms, 7(2), 171. https://doi.org/10.1242/dmm.015123 - -* Morgan, A. C., Economou, D. J., Way, S. F., & Clauset, A. (2018). Prestige drives epistemic inequality in the diffusion of scientific ideas. EPJ Data Science, 7(1), 40. https://doi.org/10.1140/epjds/s13688-018-0166-4 - -* Naudet, F., Ioannidis, J., Miedema, F., Cristea, I. A., Goodman, S. N., & Moher, D. (2018). Six principles for assessing scientists for hiring, promotion, and tenure. Impact of Social Sciences Blog. http://eprints.lse.ac.uk/90753/ - -* Pickett, C. (2017). Let's Look at the Big Picture: A System-Level Approach to Assessing Scholarly Merit. https://doi.org/10.31234/osf.io/tv6nb - -* Roediger III, H. L. (2016). Varieties of fame in psychology. Perspectives on Psychological Science, 11(6), 882-887. - -* Ruscio, J. (2016). Taking advantage of citation measures of scholarly impact: Hip Hip h Index!. Perspectives on Psychological Science, 11(6), 905-908. - -* Shiota, M. N. (2017). “Fame” is the Problem:Conflation of Visibility With Potential for Long-Term Impact in Psychological Science. https://doi.org/10.31234/osf.io/4kwuq - -* Simonton, D. K. (2016). Giving credit where credit’s due: Why it’s so hard to do in psychological science. Perspectives on Psychological Science, 11(6), 888-892. - -* Tressoldi, P. E., Giofré, D., Sella, F., & Cumming, G. (2013). High impact= high statistical standards? Not necessarily so. PloS one, 8(2), e56180. - -* Sternberg, R. J. (2016). “Am I famous yet?” Judging scholarly merit in psychological science: An introduction. Perspectives on Psychological Science, 11(6), 877-881. - -* Vazire, S. (2017). Against eminence.https://doi.org/10.31234/osf.io/djbcw - -* Van Dijk, D., Manor, O., & Carey, L. B. (2014). Publication metrics and success on the academic job market. Current Biology, 24(11), R516-R517. - -
-
- -

- -## Types of academic, non-academic & alt-academic positions - -* Gomez, P., Anderson, A. R., & Baciero, A. (2017). Lessons for psychology laboratories from industrial laboratories. Research Ethics, 13(3-4), 155-160. https://doi.org/10.1177/1747016117693827 - -* Nature. (2019). Postdocs in crisis: science cannot risk losing the next generation. Nature, 580, 160. https://doi.org/10.1038/d41586-020-02541-9 - -* Nature. (2019). The mental health of PhD researchers demands urgent attention. Nature, 575, 257-258. https://doi.org/10.1038/d41586-019-03489-1 - -* Nature. (2020). Seeking an ‘exit plan’ for leaving academia amid coronavirus worries. Nature 583, 645-646. https://doi.org/10.1038/d41586-020-02029-6. - - -
-
- -

- -## Feminist Thought - -***It aims to understand the nature of gender inequality. Themes explored include discrimination, objectification, oppression, patriarchy, stereotyping, and aesthetics. It examines women's and men's social roles, experiences, interests, chores, and feminist politics in a variety of fields.*** - -* Eagly, A. H., Eaton, A., Rose, S. M., Riger, S., & McHugh, M. C. (2012). Feminism and psychology: Analysis of a half-century of research on women and gender. American Psychologist, 67(3), 211-230, https://doi.org/10.1037/a0027260 - -* Matsick, J. L., Kruk, M., Oswald, F., & Palmer, L. (2021). Bridging Feminist Psychology and Open Science: Feminist Tools and Shared Values Inform Best Practices for Science Reform. Psychology of Women Quarterly, https://doi.org/10.1177/03616843211026564 - -* Lazard, L., & McAvoy, J. (2020). Doing reflexivity in psychological research: What’s the point? What’s the practice?. Qualitative research in psychology, 17(2), 159-177 https://doi.org/10.1080/14780887.2017.1400144 - -* Macleod, C. I., Capdevila, R., Marecek, J., Braun, V., Gavey, N., & Wilkinson, S. (2021). Celebrating 30 years of Feminism & Psychology. Feminism & Psychology, 31(3), 313-325. https://doi.org/10.1177/09593535211027457 - -* Crawford, M., & Marecek, J. (1989). Feminist theory, feminist psychology: A bibliography of epistemology, critical analysis, and applications. Psychology of Women Quarterly, 13(4), 477-491. https://doi.org/10.1111/j.1471-6402.1989.tb01015.x - -* Marecek, J. (2016). Invited reflection: Intersectionality theory and feminist psychology. Psychology of Women Quarterly, 40(2), 177-181. https://doi.org/10.1177/0361684316641090 - -* OpenSexism Archives on Open Science https://opensexism.wordpress.com/tag/open-science/ - -
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- -
diff --git a/content/clusters/clusters-data.md b/content/clusters/clusters-data.md deleted file mode 100644 index 68c897e1dd4..00000000000 --- a/content/clusters/clusters-data.md +++ /dev/null @@ -1,21 +0,0 @@ -+++ -widget = "blank" -headless = true -active = true -weight = 10 - -title = "" -subtitle = "" - -[design] - columns = "1" - -[design.spacing] - padding = ["20px", "0", "60px", "0"] - -[advanced] - css_style = "" - css_class = "" -+++ - -{{< clusters_display >}} diff --git a/content/clusters/index.md b/content/clusters/index.md index babb5d46348..b10dbfa04b0 100644 --- a/content/clusters/index.md +++ b/content/clusters/index.md @@ -1,6 +1,9 @@ +++ -# FORRT page -type = "widget_page" -headless = false # Homepage is headless, other widget pages are not. -title = "Clusters" +# FORRT Clusters +title = "FORRT's Clusters" +description = "Comprehensive taxonomy of Open and Reproducible Science concepts with 11 interconnected clusters" + +# Optional metadata +date = 2024-01-01 +draft = false +++ diff --git a/content/clusters/intro-clusters.md b/content/clusters/intro-clusters.md deleted file mode 100644 index 91c322dda59..00000000000 --- a/content/clusters/intro-clusters.md +++ /dev/null @@ -1,88 +0,0 @@ -+++ -# A Demo section created with the Blank widget. -# Any elements can be added in the body: https://sourcethemes.com/academic/docs/writing-markdown-latex/ -# Add more sections by duplicating this file and customizing to your requirements. - -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = true # Activate this widget? true/false -weight = 5 # Order that this section will appear. - -title = "" -subtitle = "" - -[design] - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "1" - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "Green" - # color = "#69b3a2" # greenish - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "headers/bubbles-wide.webp" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - # image_size = "cover" # Options are `cover` (default), `contain`, or `actual` size. - # image_position = "center" # Options include `left`, `center` (default), or `right`. - # image_parallax = true # Use a fun parallax-like fixed background effect? true/false - - # Text color (true=light or false=dark). - text_color_light = false - -[design.spacing] - # Customize the section spacing. Order is top, right, bottom, left. - padding = ["60px", "0", "60px", "0"] - -[advanced] - # Custom CSS. - css_style = "font-size: 1.25rem;" - - # CSS class. - css_class = "" -+++ - -# FORRT's Clusters - -
- -In order to teach Open and Reproducible Science effectively, educators need to make sense of almost a decade of literature, across several fields, and be informed about ongoing (and often dynamic) debates. This is a tall ask for most educators. So FORRT sought to develop strategies and propose solutions to mitigate the effects of competing academic interests and help scholars implement open and reproducible science tenets in their teaching and mentoring workflow. In an effort to reduce some of the burden on educators wishing to learn or teach these concepts, FORRT has drawn on the expertise of more than 50 experts from its community to provide educators with a comprehensive but straightforward accessible didactic framework. FORRT clusters is a result of a comprehensive literature review guided by educational, pedagogical and didactic considerations aiming at providing a pathway towards the incremental adoption of Open and Reproducible Science tenets into educators/scholars teaching and mentoring. The focus lies not on simply aggregating the literature into bins, but on making sense of existing works, weaving connections where none exist, and providing a sensible learning-oriented Open and Reproducible Science taxonomy. FORRT taxonomy is composed of 11 clusters: - -1. Replicability crisis and credibility revolution knowledge -2. Conceptual and statistical knowledge -3. Ways of working -4. Pre-analysis planning -5. Transparency and reproducibility in computation and analysis -6. FAIR data and materials -7. Publication sharing -8. Replication and meta-research -9. Academic structures and institutions -10. Qualitative Research -11. Research Integrity - -These clusters contain information for quantitative and qualitative researchers. - -We further break down each cluster into sub-categories to provide educators/scholars with useful information on the extent of open scholarship, and how they are connected to one another. The idea behind specifying clusters and sub-clusters is to highlight that we have drawn fuzzy boundaries between clusters, while allowing for diversification and heterogeneity in how each educator integrates these cluster/sub-clusters with their respective field content. The breakdown of each cluster into sub-categories provides scholars with useful information on the extent of open science scholarship, and how they are connected to one another. - - -See below for each cluster, its description, sub-clusters, and associated works geared for teaching. And here's an attempt to visualize FORRT's clusters: -
- -![FORRT's Clusters](FORRT_Clusters.webp "FORRT's Clusters") - -
- -## FORRT's Syllabus {#Syllabus} - -Building on the clusters we created a ***"Open and Reproducible Science" Syllabus***. We hope it can serve as a starting point for your class. [.pdf download](FORRT_O&R_101_Syllabus.pdf) or [editable G-doc version](https://docs.google.com/document/d/1pfFro5MbwBHzzXTeM_lE1gjFuq7AnnKWSDWkVwOBAtE/edit#). Check out the [FORRT's syllabus page](/syllabus/). - -
diff --git a/layouts/clusters/list.html b/layouts/clusters/list.html new file mode 100644 index 00000000000..5ebc8e911f4 --- /dev/null +++ b/layouts/clusters/list.html @@ -0,0 +1,44 @@ +{{/* layouts/clusters/list.html - List layout for clusters section */}} +{{ define "main" }} +
+
+ + {{/* Clusters page header */}} + {{ if .Params.image }} +
+ {{ .Title }} +
+ {{ end }} + +
+

{{ .Title }}

+ + {{/* Subtitle if present */}} + {{ if .Params.subtitle }} +

{{ .Params.subtitle | markdownify }}

+ {{ end }} + + {{/* Optional section content */}} + {{ with .Content }} +
+ {{ . }} +
+ {{ end }} +
+
+
+ + {{/* CLUSTERS INTRO SECTION */}} +
+
+ {{ partial "clusters/intro.html" . }} +
+
+ + {{/* CLUSTERS DISPLAY SECTION */}} +
+
+ {{ partial "clusters/all_clusters.html" . }} +
+
+{{ end }} diff --git a/layouts/clusters/single.html b/layouts/clusters/single.html new file mode 100644 index 00000000000..5dae5ade492 --- /dev/null +++ b/layouts/clusters/single.html @@ -0,0 +1,53 @@ +{{/* layouts/clusters/single.html - Main layout for clusters page */}} +{{ define "main" }} +
+
+ + {{/* Clusters page header */}} + {{ if .Params.image }} +
+ {{ .Title }} +
+ {{ end }} + +
+

{{ .Title }}

+ + {{/* Subtitle if present */}} + {{ if .Params.subtitle }} +

{{ .Params.subtitle | markdownify }}

+ {{ end }} + + {{/* Page description/metadata */}} +
+ {{ if .Params.authors }} + + {{ with .Params.authors }} + {{ delimit . ", " }} + {{ end }} + + {{ end }} + {{ if .PublishDate }} + + {{ .PublishDate.Format "January 2, 2006" }} + + {{ end }} +
+
+
+
+ + {{/* CLUSTERS INTRO SECTION */}} +
+
+ {{ partial "clusters/intro.html" . }} +
+
+ + {{/* CLUSTERS DISPLAY SECTION - The main clusters content */}} +
+
+ {{ partial "clusters/all_clusters.html" . }} +
+
+{{ end }} diff --git a/layouts/partials/clusters/all_clusters.html b/layouts/partials/clusters/all_clusters.html new file mode 100644 index 00000000000..6bf1d26a3a0 --- /dev/null +++ b/layouts/partials/clusters/all_clusters.html @@ -0,0 +1,147 @@ +{{/* all_clusters.html - Partial to display all clusters from data */}} +{{ $data := site.Data.clusters_v4 }} +{{ if not $data }} +
+ Data Error: clusters_v4.json data not found. Run python3 scripts/parse_clusters_to_sheet.py --export-json. +
+ {{ return }} +{{ end }} + +{{ $colors := slice "#cacfdc" "#eadce6" "#d4e4d9" "#BDC5CA" "#dce4ea" "#e8ddd4" "#c9dbcb" "#d9cfe0" "#cddde3" "#e0d8cc" "#d4dce8" }} +{{ $arrowColors := slice "#6070a0" "#a05080" "#408060" "#607080" "#5080a0" "#a08060" "#509060" "#8060a0" "#5090a0" "#907050" "#6070a0" }} + +
+ +
+ {{/* ===== SEARCH BAR (above sidebar+content) ===== */}} +
+ + +
+ + {{/* ===== MOBILE NAV TOGGLE ===== */}} + +
+ +
+ {{/* ===== SIDEBAR ===== */}} +
+
+
Clusters & Sub-clusters
+ +
+
+ + {{/* ===== MAIN CONTENT ===== */}} +
+ {{ range $ci, $cluster := $data.clusters }} + {{ $cid := printf "cluster-%d" (int $cluster.number) }} + {{ $color := index $colors (mod $ci (len $colors)) }} + {{ $totalPubs := 0 }}{{ range $cluster.sub_clusters }}{{ $totalPubs = add $totalPubs (len .publications) }}{{ end }} + +
+
+

+ {{ (int $cluster.number) }} + {{ $cluster.name }} +

+ {{ len $cluster.sub_clusters }} sub-clusters · {{ $totalPubs }} references +
+ + {{ if $cluster.description }} +

{{ $cluster.description }}

+ {{ end }} + + {{/* Sub-cluster tabs */}} + {{ if gt (len $cluster.sub_clusters) 0 }} + + +
+ {{ range $si, $sc := $cluster.sub_clusters }} + {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} +
+ +

{{ $sc.name }}

+ + {{ if $sc.description }} +

{{ $sc.description }}

+ {{ end }} + + {{ if $sc.publications }} +
    + {{ range $sc.publications }} +
  • + {{ $ref := .apa }} + {{/* Strip DOI URL from text - we show it separately */}} + {{ $ref = replaceRE `\s*https?://(?:dx\.)?doi\.org/\S+` "" $ref }} + {{ $ref = replaceRE `\s+$` "" $ref }} + {{/* Strip dangerous tags but keep i/em for italics (data from doi.org is trusted) */}} + {{ $ref = replaceRE `]*>.*?` "" $ref }} + {{ $ref = replaceRE `]*>.*?` "" $ref }} + {{/* Linkify remaining URLs */}} + {{ $ref = replaceRE `(https?://\S+)` `$1` $ref }} + {{ $ref | safeHTML }} + {{ if .doi }} + {{ $doiURL := printf "https://doi.org/%s" .doi }} + {{ $doiURL }} + {{ end }} +
    • + {{ end }} +
+ {{ else }} +

No publications listed for this sub-cluster yet.

+ {{ end }} + +
+ {{ end }} +
+ {{ end }} +
+ + {{ end }} +
+
+
+ + diff --git a/layouts/partials/clusters/intro.html b/layouts/partials/clusters/intro.html new file mode 100644 index 00000000000..23a5fdd9ff0 --- /dev/null +++ b/layouts/partials/clusters/intro.html @@ -0,0 +1,78 @@ +{{/* intro.html - Intro section for clusters page with matching styling */}} +
+ + {{/* Main introductory text */}} +
+

+ In order to teach Open and Reproducible Science effectively, educators need to make sense of almost a decade of literature, across several fields, and be informed about ongoing (and often dynamic) debates. This is a tall ask for most educators. So FORRT sought to develop strategies and propose solutions to mitigate the effects of competing academic interests and help scholars implement open and reproducible science tenets in their teaching and mentoring workflow. +

+ +

+ In an effort to reduce some of the burden on educators wishing to learn or teach these concepts, FORRT has drawn on the expertise of more than 50 experts from its community to provide educators with a comprehensive but straightforward accessible didactic framework. FORRT clusters is a result of a comprehensive literature review guided by educational, pedagogical and didactic considerations aiming at providing a pathway towards the incremental adoption of Open and Reproducible Science tenets into educators/scholars teaching and mentoring. +

+ +

+ The focus lies not on simply aggregating the literature into bins, but on making sense of existing works, weaving connections where none exist, and providing a sensible learning-oriented Open and Reproducible Science taxonomy. FORRT taxonomy is composed of 11 clusters: +

+
+ + {{/* Clusters list */}} +
+
    +
  1. Replicability crisis and credibility revolution knowledge
    2. +
  2. Conceptual and statistical knowledge
    3. +
  3. Ways of working
    4. +
  4. Pre-analysis planning
    5. +
  5. Transparency and reproducibility in computation and analysis
    6. +
  6. FAIR data and materials
    7. +
  7. Publication sharing
    8. +
  8. Replication and meta-research
    9. +
  9. Academic structures and institutions
    10. +
  10. Qualitative Research
    11. +
  11. Research Integrity
    12. +
+
+ + {{/* Clusters contain info note */}} +
+

+ Note: These clusters contain information for quantitative and qualitative researchers. +

+ +

+ We further break down each cluster into sub-categories to provide educators/scholars with useful information on the extent of open scholarship, and how they are connected to one another. The idea behind specifying clusters and sub-clusters is to highlight that we have drawn fuzzy boundaries between clusters, while allowing for diversification and heterogeneity in how each educator integrates these cluster/sub-clusters with their respective field content. The breakdown of each cluster into sub-categories provides scholars with useful information on the extent of open science scholarship, and how they are connected to one another. +

+ +

+ See below for each cluster, its description, sub-clusters, and associated works geared for teaching. And here's an attempt to visualize FORRT's clusters: +

+
+ + {{/* Clusters visualization image */}} +
+
+ FORRT's Clusters hierarchy diagram +
FORRT's Clusters Overview
+
+
+ + {{/* Syllabus section */}} +
+

FORRT's Syllabus

+

+ Building on the clusters we created a "Open and Reproducible Science" Syllabus. We hope it can serve as a starting point for your class. +

+
+ + 📄 PDF Download + + + 📝 Editable G-doc + + + 📚 Syllabus Page + +
+
+ +
diff --git a/layouts/partials/custom_js.html b/layouts/partials/custom_js.html index 6483386262f..a0e630eee3e 100644 --- a/layouts/partials/custom_js.html +++ b/layouts/partials/custom_js.html @@ -1,6 +1,8 @@ {{/* Custom JavaScript for FORRT site */}} -{{/* Include clusters search functionality on clusters page */}} -{{ if eq .RelPermalink "/clusters/" }} +{{/* Clusters list page lives at content/clusters/index.md — Section is often empty; match by path */}} +{{ $isClustersPage := and .File (strings.HasPrefix .File.Path "clusters/") }} +{{ if $isClustersPage }} + {{ end }} diff --git a/layouts/shortcodes/clusters_display.html b/layouts/shortcodes/clusters_display.html deleted file mode 100644 index 98cc5f80ad6..00000000000 --- a/layouts/shortcodes/clusters_display.html +++ /dev/null @@ -1,367 +0,0 @@ -{{/* clusters_display.html - Renders all FORRT clusters from data/clusters_v4.json */}} -{{ $data := site.Data.clusters_v4 }} -{{ if not $data }} -

Error: clusters_v4.json data not found. Run python3 scripts/parse_clusters_to_sheet.py --export-json.

- {{ return }} -{{ end }} - -{{ $colors := slice "#cacfdc" "#eadce6" "#d4e4d9" "#BDC5CA" "#dce4ea" "#e8ddd4" "#c9dbcb" "#d9cfe0" "#cddde3" "#e0d8cc" "#d4dce8" }} -{{ $arrowColors := slice "#6070a0" "#a05080" "#408060" "#607080" "#5080a0" "#a08060" "#509060" "#8060a0" "#5090a0" "#907050" "#6070a0" }} - -
- - {{/* ===== SEARCH BAR (above sidebar+content) ===== */}} -
- - -
- - {{/* ===== MOBILE NAV TOGGLE ===== */}} - - -
- {{/* ===== SIDEBAR ===== */}} -
-
-
Clusters & Sub-clusters
- -
-
- - {{/* ===== MAIN CONTENT ===== */}} -
- {{ range $ci, $cluster := $data.clusters }} - {{ $cid := printf "cluster-%d" (int $cluster.number) }} - {{ $color := index $colors (mod $ci (len $colors)) }} - {{ $totalPubs := 0 }}{{ range $cluster.sub_clusters }}{{ $totalPubs = add $totalPubs (len .publications) }}{{ end }} - -
-
-

- {{ (int $cluster.number) }} - {{ $cluster.name }} -

- {{ len $cluster.sub_clusters }} sub-clusters · {{ $totalPubs }} references -
- - {{ if $cluster.description }} -

{{ $cluster.description }}

- {{ end }} - - {{/* Sub-cluster tabs */}} - {{ if gt (len $cluster.sub_clusters) 0 }} - - -
- {{ range $si, $sc := $cluster.sub_clusters }} - {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} -
- -

{{ $sc.name }}

- - {{ if $sc.description }} -

{{ $sc.description }}

- {{ end }} - - {{ if $sc.publications }} -
    - {{ range $sc.publications }} -
  • - {{ $ref := .apa }} - {{/* Strip DOI URL from text - we show it separately */}} - {{ $ref = replaceRE `\s*https?://(?:dx\.)?doi\.org/\S+` "" $ref }} - {{ $ref = replaceRE `\s+$` "" $ref }} - {{/* Strip dangerous tags but keep i/em for italics (data from doi.org is trusted) */}} - {{ $ref = replaceRE `]*>.*?` "" $ref }} - {{ $ref = replaceRE `]*>.*?` "" $ref }} - {{/* Linkify remaining URLs */}} - {{ $ref = replaceRE `(https?://\S+)` `$1` $ref }} - {{ $ref | safeHTML }} - {{ if .doi }} - {{ $doiURL := printf "https://doi.org/%s" .doi }} - {{ $doiURL }} - {{ end }} -
    • - {{ end }} -
- {{ else }} -

No publications listed for this sub-cluster yet.

- {{ end }} - -
- {{ end }} -
- {{ end }} -
- - {{ end }} -
-
-
- -{{/* ===== JAVASCRIPT ===== */}} - diff --git a/static/js/clusters-page.js b/static/js/clusters-page.js new file mode 100644 index 00000000000..5d834ce89e3 --- /dev/null +++ b/static/js/clusters-page.js @@ -0,0 +1,176 @@ +/** + * Clusters page: sticky layout metrics, nav, embedded search, back-to-top. + * Requires .clusters-layout (from layouts/partials/clusters/all_clusters.html). + */ +(function () { + 'use strict'; + + function onReady(fn) { + if (document.readyState === 'loading') { + document.addEventListener('DOMContentLoaded', fn); + } else { + fn(); + } + } + + function getNavbarStickyOffsetPx() { + var bodyTop = parseFloat(window.getComputedStyle(document.body).marginTop) || 0; + var navbar = document.getElementById('navbar-main'); + if (!navbar) return bodyTop; + var bottom = Math.ceil(navbar.getBoundingClientRect().bottom); + return Math.max(bottom, bodyTop); + } + + function performClustersSearch(query, resultsContainer) { + var results = []; + document.querySelectorAll('.cluster-section').forEach(function (section) { + if (section.textContent.toLowerCase().indexOf(query) === -1) return; + var titleEl = section.querySelector('.cluster-title'); + results.push({ + id: section.id, + title: titleEl ? titleEl.textContent.trim() : section.id + }); + }); + + if (results.length === 0) { + resultsContainer.innerHTML = '
No results found.
'; + } else { + var html = '
' + results.length + ' result' + + (results.length !== 1 ? 's' : '') + '
'; + results.slice(0, 10).forEach(function (r) { + html += '' + + escapeHtml(r.title) + ''; + }); + if (results.length > 10) { + html += '
... and ' + (results.length - 10) + ' more results.
'; + } + resultsContainer.innerHTML = html; + } + resultsContainer.style.display = 'block'; + } + + function escapeHtml(s) { + var d = document.createElement('div'); + d.textContent = s; + return d.innerHTML; + } + + onReady(function () { + var root = document.querySelector('.clusters-layout'); + if (!root) return; + + var mobileToggle = document.getElementById('clusters-mobile-toggle'); + var sidebar = document.getElementById('clusters-sidebar'); + var backToTopBtn = document.getElementById('clusters-back-to-top'); + var controls = root.querySelector('.clusters-controls'); + var navbarEl = document.getElementById('navbar-main'); + + function updateStickyLayoutMetrics() { + if (!controls) return; + root.style.setProperty('--clusters-sticky-offset', getNavbarStickyOffsetPx() + 'px'); + root.style.setProperty('--clusters-controls-height', controls.offsetHeight + 'px'); + } + + function scheduleStickyLayoutMetrics() { + updateStickyLayoutMetrics(); + requestAnimationFrame(function () { + updateStickyLayoutMetrics(); + }); + } + + scheduleStickyLayoutMetrics(); + window.addEventListener('resize', scheduleStickyLayoutMetrics, { passive: true }); + window.addEventListener('orientationchange', scheduleStickyLayoutMetrics, { passive: true }); + if (window.ResizeObserver && navbarEl) { + new ResizeObserver(scheduleStickyLayoutMetrics).observe(navbarEl); + } + + if (mobileToggle && sidebar) { + mobileToggle.addEventListener('click', function () { + sidebar.classList.toggle('sidebar-open'); + this.classList.toggle('active'); + scheduleStickyLayoutMetrics(); + }); + } + + root.querySelectorAll('.cluster-nav-heading').forEach(function (heading) { + heading.addEventListener('click', function (e) { + e.preventDefault(); + var group = this.closest('.cluster-nav-group'); + if (!group) return; + var subList = group.querySelector('.cluster-nav-subs'); + var arrow = group.querySelector('.cluster-nav-toggle'); + if (!subList || !arrow) return; + var isHidden = subList.style.display === 'none'; + subList.style.display = isHidden ? 'block' : 'none'; + arrow.innerHTML = isHidden ? '▾' : '▸'; + var clusterId = group.getAttribute('data-cluster'); + var section = clusterId ? document.getElementById(clusterId) : null; + if (section) section.scrollIntoView({ behavior: 'smooth', block: 'start' }); + }); + }); + + root.querySelectorAll('.sc-nav-link').forEach(function (link) { + link.addEventListener('click', function (e) { + e.preventDefault(); + var clusterId = this.getAttribute('data-cluster'); + var tabId = this.getAttribute('data-tab'); + var section = clusterId ? document.getElementById(clusterId) : null; + if (section && tabId) { + var tab = document.getElementById(tabId); + if (tab) { + if (typeof window.jQuery !== 'undefined' && window.jQuery.fn.tab) { + window.jQuery(tab).tab('show'); + } else { + tab.click(); + } + } + setTimeout(function () { + section.scrollIntoView({ behavior: 'smooth', block: 'start' }); + }, 100); + } + if (sidebar) sidebar.classList.remove('sidebar-open'); + if (mobileToggle) mobileToggle.classList.remove('active'); + }); + }); + + var searchInput = document.getElementById('cluster-search'); + var searchResults = document.getElementById('cluster-search-results'); + var debounceTimer; + + if (searchInput && searchResults) { + searchInput.addEventListener('input', function () { + clearTimeout(debounceTimer); + var query = this.value.toLowerCase().trim(); + if (query.length < 2) { + searchResults.style.display = 'none'; + searchResults.innerHTML = ''; + return; + } + debounceTimer = setTimeout(function () { + performClustersSearch(query, searchResults); + }, 200); + }); + + searchResults.addEventListener('click', function (e) { + var link = e.target.closest('.search-result-item'); + if (!link) return; + e.preventDefault(); + var targetId = link.getAttribute('data-target'); + var target = targetId ? document.getElementById(targetId) : null; + if (target) target.scrollIntoView({ behavior: 'smooth', block: 'start' }); + }); + } + + if (backToTopBtn) { + function toggleBackToTop() { + backToTopBtn.classList.toggle('is-visible', window.scrollY > 500); + } + window.addEventListener('scroll', toggleBackToTop, { passive: true }); + toggleBackToTop(); + backToTopBtn.addEventListener('click', function () { + window.scrollTo({ top: 0, behavior: 'smooth' }); + }); + } + }); +})(); From 2f3a56bd6dfb990a1e2af47d99c9220c4a96b119 Mon Sep 17 00:00:00 2001 From: richarddushime Date: Mon, 23 Mar 2026 21:45:47 +0100 Subject: [PATCH 05/11] rm: left custom search, enhancement of the UI --- assets/scss/custom.scss | 258 ++++++-- layouts/partials/clusters/all_clusters.html | 18 +- layouts/partials/clusters/intro.html | 2 +- layouts/partials/custom_js.html | 3 +- static/js/clusters-page.js | 408 +++++++++++-- static/js/clusters-search.js | 637 -------------------- 6 files changed, 567 insertions(+), 759 deletions(-) delete mode 100644 static/js/clusters-search.js diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index 3b3e9245f14..273fa701a32 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -233,63 +233,154 @@ margin-bottom: 0.75rem; } -/* ---- Search bar ---- */ -.clusters-search-bar { +/* ---- Inline clusters list search (toolbar; not Algolia/site search) ---- */ +.clusters-inline-search { position: relative; } -.clusters-search-bar .form-control { - font-size: 0.9rem; - padding: 0.5rem 0.75rem; +.clusters-inline-search__row { + display: flex; + flex-wrap: nowrap; + align-items: stretch; + gap: 0.4rem; + position: relative; + z-index: 2; + background: #fefdf6; + padding-bottom: 0.45rem; +} + +.clusters-inline-search__input { + flex: 1 1 auto; + min-width: 0; + max-width: 22rem; + font-size: 0.88rem; + padding: 0.45rem 0.65rem; border-radius: 6px; } -.cluster-search-results { - max-height: 350px; - overflow-y: auto; +.clusters-inline-search__submit { + flex: 0 0 auto; + display: inline-flex; + align-items: center; + justify-content: center; + min-width: 2.35rem; + padding: 0.35rem 0.55rem; + border-radius: 6px; +} + +.clusters-inline-search__toolbar { + display: flex; + align-items: center; + justify-content: space-between; + gap: 0.5rem; + padding: 0.35rem 0.5rem 0.35rem 0.75rem; +} + +.clusters-inline-search__close { + flex-shrink: 0; + line-height: 1; + padding: 0.25rem 0.45rem !important; +} + +/* Like browser Ctrl+F: flat highlight, no ring/border */ +.clusters-inline-search-highlight { + outline: none !important; + box-shadow: none !important; + background-color: rgba(255, 220, 0, 0.55) !important; + border-radius: 2px; + transition: background-color 0.35s ease; +} + +/* Panel below input row: toolbar fixed, only hit list scrolls (no overlap with search box) */ +.clusters-inline-search__panel { + display: none; + flex-direction: column; + width: 100%; + max-height: 360px; + margin-top: 0.75rem; background: #fff; border: 1px solid #ddd; border-radius: 6px; - margin-top: 0.25rem; + box-shadow: 0 6px 20px rgba(0, 0, 0, 0.08); + overflow: hidden; + position: relative; + z-index: 1; } -.search-count { - font-size: 0.72rem; - color: #888; - padding: 0.4rem 0.75rem; +.clusters-inline-search__panel.clusters-inline-search__panel--open { + display: flex; +} + +.clusters-inline-search__toolbar-host { + flex-shrink: 0; border-bottom: 1px solid #eee; + background: #fafafa; } -.search-result-item { - display: block; +.clusters-inline-search__results-body { + flex: 1 1 auto; + min-height: 0; + overflow-x: hidden; + overflow-y: auto; + -webkit-overflow-scrolling: touch; +} + +.clusters-inline-search__count { + font-size: 0.72rem; + color: #666; + font-weight: 600; + margin: 0; +} + +.clusters-inline-search__hit { + display: flex; + flex-direction: column; + align-items: flex-start; + gap: 0.2rem; padding: 0.5rem 0.75rem; border-bottom: 1px solid #f0f0f0; color: #333; text-decoration: none; font-size: 0.8rem; + text-align: left; } -.search-result-item:hover { +.clusters-inline-search__hit-label { + line-height: 1.35; +} + +.clusters-inline-search__hit-meta { + font-size: 0.68rem; + color: #888; + line-height: 1.25; +} + +.clusters-inline-search__hit:hover { background: #f5f7fa; text-decoration: none; color: #111; } -.search-no-results, .search-more { +.clusters-inline-search__empty, +.clusters-inline-search__more { padding: 0.5rem 0.75rem; font-size: 0.78rem; color: #888; } -/* ---- Sub-cluster tabs (styled like real tabs) ---- */ +/* ---- Sub-cluster tabs (chip style + border: same on desktop & mobile) ---- */ .cluster-tabs { flex-wrap: wrap; + gap: 0.35rem 0.3rem; margin-bottom: 0; - border-bottom: 1px solid rgba(0,0,0,0.15); + overflow: visible; + align-items: stretch; + border-bottom: none; } .cluster-tabs .nav-item { - flex-shrink: 0; + flex: 0 1 auto; + min-width: 0; max-width: 100%; } @@ -297,25 +388,34 @@ font-size: 0.78rem; padding: 0.4rem 0.75rem; color: #8b0000; - border: 1px solid transparent; - border-bottom: none; - margin-bottom: -1px; white-space: normal; word-break: break-word; - border-radius: 4px 4px 0 0; - transition: background 0.15s, color 0.15s; + hyphens: auto; + text-align: center; + line-height: 1.25; + min-height: 2.35rem; + display: flex; + align-items: center; + justify-content: center; + flex-wrap: wrap; + gap: 0.15rem; + margin-bottom: 0; + border-radius: 6px; + border: 1px solid rgba(0, 0, 0, 0.1); + transition: background 0.15s, color 0.15s, border-color 0.15s; } .cluster-tabs .nav-link:hover { color: #5a0000; - background: rgba(255,255,255,0.5); + background: rgba(255, 255, 255, 0.5); + border-color: rgba(0, 0, 0, 0.14); } .cluster-tabs .nav-link.active { color: #000; font-weight: 600; - background: rgba(255,255,255,0.7); - border-color: rgba(0,0,0,0.15); + background: rgba(255, 255, 255, 0.88); + border-color: rgba(0, 0, 0, 0.2); } .tab-count { @@ -327,6 +427,8 @@ .cluster-tab-content { padding: 1.25rem 0.5rem; + border-top: 1px solid rgba(0, 0, 0, 0.1); + margin-top: 0.35rem; } /* ---- Sub-cluster heading & description ---- */ @@ -372,8 +474,8 @@ padding: 0.4rem; } - .cluster-search-results { - max-height: 42vh; + .clusters-inline-search__panel { + max-height: 320px; } .cluster-section { @@ -387,6 +489,12 @@ } @media (max-width: 991px) { + /* Flush under sticky controls (no mb-3 gap) + drawer meets toggle bar */ + .clusters-layout .clusters-controls { + margin-bottom: 0 !important; + } + + /* In-flow sidebar hidden until open; when open use fixed drawer so it stays visible after page scroll */ .clusters-sidebar-inner { position: static; max-height: 50vh; @@ -400,28 +508,59 @@ } .clusters-sidebar.sidebar-open { - background: #fff; - border: 1px solid #e9ecef; - border-radius: 8px; - padding: 0.5rem; - margin-bottom: 0.75rem; - } - - .cluster-tabs { - flex-wrap: nowrap; - overflow-x: auto; - overflow-y: hidden; + display: block; + position: fixed; + left: 0; + right: 0; + width: 100%; + max-width: 100vw; + margin: 0; + padding: 0 0.75rem calc(0.75rem + env(safe-area-inset-bottom, 0px)); + box-sizing: border-box; + top: calc( + var(--clusters-sticky-offset) + + env(safe-area-inset-top, 0px) + + var(--clusters-sticky-gap) + + var(--clusters-controls-height) + ); + bottom: 0; + z-index: 1010; + overflow-y: auto; + overflow-x: hidden; -webkit-overflow-scrolling: touch; - scrollbar-width: thin; + overscroll-behavior: contain; + background: #fefdf6; + border-top: 1px solid #e9ecef; + box-shadow: 0 -4px 24px rgba(0, 0, 0, 0.12); + border-radius: 0; } + .clusters-sidebar.sidebar-open .clusters-sidebar-inner { + position: static; + max-height: none; + margin-bottom: 0; + margin-top: 0; + overflow: visible; + padding-top: 0; + border-radius: 0; + border: none; + border-bottom: 1px solid #e9ecef; + } + + .clusters-sidebar.sidebar-open .sidebar-header { + position: sticky; + top: 0; + z-index: 1; + background: #f8f9fa; + padding: 0.15rem 0.1rem 0.45rem; + border-bottom: 1px solid #e9ecef; + margin-bottom: 0.5rem; + } + + /* Narrow screens: sized tab cells (base styles = borders match desktop) */ .cluster-tabs .nav-item { - max-width: none; - } - - .cluster-tabs .nav-link { - white-space: nowrap; - word-break: normal; + flex: 1 1 auto; + min-width: clamp(7rem, 42vw, 11.5rem); } .cluster-tab-content { @@ -435,13 +574,13 @@ box-shadow: 0 2px 8px rgba(0, 0, 0, 0.05); } - .clusters-search-bar .form-control { + .clusters-inline-search__input { font-size: 0.86rem; padding: 0.46rem 0.62rem; } - .cluster-search-results { - max-height: 38vh; + .clusters-inline-search__panel { + max-height: 280px; } .cluster-section { @@ -510,13 +649,14 @@ border-radius: 5px; } - .clusters-search-bar .form-control { + .clusters-inline-search__input { font-size: 0.82rem; padding: 0.42rem 0.55rem; + max-width: 100%; } - .cluster-search-results { - max-height: 34vh; + .clusters-inline-search__panel { + max-height: 240px; } .clusters-mobile-toggle { @@ -557,14 +697,15 @@ margin-top: 0.45rem; } - .cluster-tabs { - scroll-padding-left: 0.25rem; + .cluster-tabs .nav-item { + min-width: calc(50% - 0.2rem); + flex: 1 1 calc(50% - 0.2rem); } .cluster-tabs .nav-link { font-size: 0.66rem; min-height: 1.9rem; - border-radius: 3px 3px 0 0; + border-radius: 5px; } .cluster-tab-content { @@ -1361,9 +1502,6 @@ article.article:has(table) .article-container { margin-top: 1rem; margin-bottom: 0; padding: 0.85rem 1.25rem 1.15rem; - background: #f8f9fa; - border-radius: 8px; - border: 1px solid #e9ecef; } .syllabus-heading { diff --git a/layouts/partials/clusters/all_clusters.html b/layouts/partials/clusters/all_clusters.html index 6bf1d26a3a0..0fe9ee2599a 100644 --- a/layouts/partials/clusters/all_clusters.html +++ b/layouts/partials/clusters/all_clusters.html @@ -13,11 +13,19 @@
- {{/* ===== SEARCH BAR (above sidebar+content) ===== */}} -
- - + {{/* Inline cluster list search (not site search; JS: static/js/clusters-page.js) */}} +
+
+ + +
+
+ +
+
{{/* ===== MOBILE NAV TOGGLE ===== */}} diff --git a/layouts/partials/clusters/intro.html b/layouts/partials/clusters/intro.html index 23a5fdd9ff0..0a4ac4d1740 100644 --- a/layouts/partials/clusters/intro.html +++ b/layouts/partials/clusters/intro.html @@ -69,7 +69,7 @@

FORRT's Syllabus

📝 Editable G-doc - + 📚 Syllabus Page
diff --git a/layouts/partials/custom_js.html b/layouts/partials/custom_js.html index a0e630eee3e..be17bee3775 100644 --- a/layouts/partials/custom_js.html +++ b/layouts/partials/custom_js.html @@ -1,8 +1,7 @@ {{/* Custom JavaScript for FORRT site */}} -{{/* Clusters list page lives at content/clusters/index.md — Section is often empty; match by path */}} +{{/* Clusters page: load after DOM; defer runs before DOMContentLoaded so onReady still fires */}} {{ $isClustersPage := and .File (strings.HasPrefix .File.Path "clusters/") }} {{ if $isClustersPage }} - {{ end }} diff --git a/static/js/clusters-page.js b/static/js/clusters-page.js index 5d834ce89e3..3483774f965 100644 --- a/static/js/clusters-page.js +++ b/static/js/clusters-page.js @@ -1,10 +1,60 @@ /** - * Clusters page: sticky layout metrics, nav, embedded search, back-to-top. - * Requires .clusters-layout (from layouts/partials/clusters/all_clusters.html). + * Clusters page: sticky layout, cluster nav, inline toolbar search, back-to-top. + * Search: clusters & sub-clusters — matches title, stats line (sub-clusters / references), and descriptions. */ (function () { 'use strict'; + var MAX_RESULTS = 400; + var SHOWN_RESULTS = 80; + var RESULTS_OPEN_CLASS = 'clusters-inline-search__panel--open'; + var HIGHLIGHT_CLASS = 'clusters-inline-search-highlight'; + var HIGHLIGHT_DURATION_MS = 60 * 1000; /* 1 minute */ + + function tokenizeQuery(q) { + return q + .toLowerCase() + .trim() + .split(/\s+/) + .filter(function (t) { + return t.length > 0; + }); + } + + /** Every token must appear somewhere in text (supports long multi-word queries). */ + function matchesAllTokens(text, tokens) { + if (!tokens.length) return false; + var lower = String(text).toLowerCase(); + for (var i = 0; i < tokens.length; i++) { + if (lower.indexOf(tokens[i]) === -1) return false; + } + return true; + } + + /** Text used to match cluster rows (title + stats + description — not only the heading). */ + function getClusterSectionSearchText(section) { + if (!section) return ''; + var parts = []; + var titleEl = section.querySelector('.cluster-title'); + if (titleEl) parts.push(titleEl.textContent); + var statsEl = section.querySelector('.cluster-stats'); + if (statsEl) parts.push(statsEl.textContent); + var descEl = section.querySelector('.cluster-description'); + if (descEl) parts.push(descEl.textContent); + return parts.join(' ').replace(/\s+/g, ' ').trim(); + } + + /** Text used to match a sub-cluster pane (heading + description). */ + function getSubclusterPaneSearchText(pane) { + if (!pane) return ''; + var parts = []; + var heading = pane.querySelector('.sc-heading'); + if (heading) parts.push(heading.textContent); + var descEl = pane.querySelector('.sc-description'); + if (descEl) parts.push(descEl.textContent); + return parts.join(' ').replace(/\s+/g, ' ').trim(); + } + function onReady(fn) { if (document.readyState === 'loading') { document.addEventListener('DOMContentLoaded', fn); @@ -21,38 +71,124 @@ return Math.max(bottom, bodyTop); } - function performClustersSearch(query, resultsContainer) { + function escapeHtml(s) { + var d = document.createElement('div'); + d.textContent = s; + return d.innerHTML; + } + + function showBootstrapTab(tabEl) { + if (!tabEl) return; + if (typeof window.jQuery !== 'undefined' && window.jQuery.fn.tab) { + window.jQuery(tabEl).tab('show'); + } else { + tabEl.click(); + } + } + + function collectClustersInlineSearchResults(scopeRoot, tokens) { var results = []; - document.querySelectorAll('.cluster-section').forEach(function (section) { - if (section.textContent.toLowerCase().indexOf(query) === -1) return; + var seen = {}; + + function add(key, item) { + if (results.length >= MAX_RESULTS || seen[key]) return; + seen[key] = true; + results.push(item); + } + + if (!scopeRoot || !tokens.length) return results; + + scopeRoot.querySelectorAll('.cluster-section').forEach(function (section) { + if (results.length >= MAX_RESULTS) return; + var clusterId = section.id; var titleEl = section.querySelector('.cluster-title'); - results.push({ - id: section.id, - title: titleEl ? titleEl.textContent.trim() : section.id + var clusterName = titleEl ? titleEl.textContent.replace(/\s+/g, ' ').trim() : clusterId; + var clusterHaystack = getClusterSectionSearchText(section); + + if (matchesAllTokens(clusterHaystack, tokens)) { + add('c:' + clusterId, { + type: 'cluster', + clusterId: clusterId, + tabId: '', + paneId: '', + label: clusterName, + meta: 'Cluster' + }); + } + + section.querySelectorAll('.tab-pane').forEach(function (pane) { + if (results.length >= MAX_RESULTS) return; + var paneId = pane.id; + if (!paneId) return; + var tabId = pane.getAttribute('aria-labelledby') || ''; + + var scHeading = pane.querySelector('.sc-heading'); + var scName = scHeading ? scHeading.textContent.replace(/\s+/g, ' ').trim() : ''; + var paneHaystack = getSubclusterPaneSearchText(pane); + + if (paneHaystack && matchesAllTokens(paneHaystack, tokens)) { + add('sc:' + clusterId + ':' + paneId, { + type: 'subcluster', + clusterId: clusterId, + tabId: tabId, + paneId: paneId, + label: scName, + meta: clusterName + }); + } }); }); + return results; + } + + function escAttr(s) { + return String(s == null ? '' : s).replace(/&/g, '&').replace(/"/g, '"'); + } + + function buildResultsToolbar(countText) { + return ( + '
' + + '' + countText + '' + + '' + + '
' + ); + } + + function renderClustersInlineResults(results, toolbarEl, bodyEl) { + if (!toolbarEl || !bodyEl) return; + if (results.length === 0) { - resultsContainer.innerHTML = '
No results found.
'; - } else { - var html = '
' + results.length + ' result' + - (results.length !== 1 ? 's' : '') + '
'; - results.slice(0, 10).forEach(function (r) { - html += '' + - escapeHtml(r.title) + ''; - }); - if (results.length > 10) { - html += '
... and ' + (results.length - 10) + ' more results.
'; - } - resultsContainer.innerHTML = html; + toolbarEl.innerHTML = buildResultsToolbar('0 results'); + toolbarEl.hidden = false; + bodyEl.innerHTML = '
No results found.
'; + return; } - resultsContainer.style.display = 'block'; - } - function escapeHtml(s) { - var d = document.createElement('div'); - d.textContent = s; - return d.innerHTML; + var shown = results.slice(0, SHOWN_RESULTS); + var countText = results.length + ' result' + (results.length !== 1 ? 's' : ''); + toolbarEl.innerHTML = buildResultsToolbar(countText); + toolbarEl.hidden = false; + + var html = '
'; + shown.forEach(function (r) { + html += '' + + '' + escapeHtml(r.label) + '' + + '' + escapeHtml(r.meta) + '' + + ''; + }); + html += '
'; + + if (results.length > shown.length) { + html += '
… and ' + (results.length - shown.length) + ' more. Refine your search.
'; + } + + bodyEl.innerHTML = html; } onReady(function () { @@ -64,6 +200,27 @@ var backToTopBtn = document.getElementById('clusters-back-to-top'); var controls = root.querySelector('.clusters-controls'); var navbarEl = document.getElementById('navbar-main'); + var mobileNavMq = window.matchMedia ? window.matchMedia('(max-width: 991.98px)') : null; + + function clustersNavIsMobileWidth() { + return mobileNavMq && mobileNavMq.matches; + } + + /** Keep drawer below sticky controls; release body scroll when closed or desktop. */ + function syncClustersMobileBodyScrollLock() { + if (!sidebar) return; + if (!clustersNavIsMobileWidth() || !sidebar.classList.contains('sidebar-open')) { + document.body.style.overflow = ''; + } else { + document.body.style.overflow = 'hidden'; + } + } + + function closeClustersMobileSidebar() { + if (sidebar) sidebar.classList.remove('sidebar-open'); + if (mobileToggle) mobileToggle.classList.remove('active'); + syncClustersMobileBodyScrollLock(); + } function updateStickyLayoutMetrics() { if (!controls) return; @@ -79,17 +236,31 @@ } scheduleStickyLayoutMetrics(); - window.addEventListener('resize', scheduleStickyLayoutMetrics, { passive: true }); - window.addEventListener('orientationchange', scheduleStickyLayoutMetrics, { passive: true }); + window.addEventListener( + 'resize', + function () { + scheduleStickyLayoutMetrics(); + syncClustersMobileBodyScrollLock(); + }, + { passive: true } + ); + window.addEventListener( + 'orientationchange', + function () { + scheduleStickyLayoutMetrics(); + syncClustersMobileBodyScrollLock(); + }, + { passive: true } + ); if (window.ResizeObserver && navbarEl) { new ResizeObserver(scheduleStickyLayoutMetrics).observe(navbarEl); } - if (mobileToggle && sidebar) { mobileToggle.addEventListener('click', function () { sidebar.classList.toggle('sidebar-open'); this.classList.toggle('active'); scheduleStickyLayoutMetrics(); + syncClustersMobileBodyScrollLock(); }); } @@ -104,6 +275,9 @@ var isHidden = subList.style.display === 'none'; subList.style.display = isHidden ? 'block' : 'none'; arrow.innerHTML = isHidden ? '▾' : '▸'; + /* Arrow: expand/collapse only — keep mobile drawer open for sub-cluster picks */ + var clickedArrow = e.target.closest('.cluster-nav-toggle'); + if (clickedArrow) return; var clusterId = group.getAttribute('data-cluster'); var section = clusterId ? document.getElementById(clusterId) : null; if (section) section.scrollIntoView({ behavior: 'smooth', block: 'start' }); @@ -118,48 +292,174 @@ var section = clusterId ? document.getElementById(clusterId) : null; if (section && tabId) { var tab = document.getElementById(tabId); - if (tab) { - if (typeof window.jQuery !== 'undefined' && window.jQuery.fn.tab) { - window.jQuery(tab).tab('show'); - } else { - tab.click(); - } - } + showBootstrapTab(tab); setTimeout(function () { section.scrollIntoView({ behavior: 'smooth', block: 'start' }); }, 100); } - if (sidebar) sidebar.classList.remove('sidebar-open'); - if (mobileToggle) mobileToggle.classList.remove('active'); + closeClustersMobileSidebar(); }); }); - var searchInput = document.getElementById('cluster-search'); - var searchResults = document.getElementById('cluster-search-results'); + var searchInput = document.getElementById('clusters-inline-search-input'); + var searchBtn = document.getElementById('clusters-inline-search-btn'); + var searchPanel = document.getElementById('clusters-inline-search-panel'); + var searchToolbar = document.getElementById('clusters-inline-search-toolbar'); + var searchResults = document.getElementById('clusters-inline-search-results'); var debounceTimer; + var searchRoot = searchInput ? searchInput.closest('.clusters-inline-search') : null; + var highlightClearTimer; + + function clearClusterSearchHighlights() { + root.querySelectorAll('.' + HIGHLIGHT_CLASS).forEach(function (el) { + el.classList.remove(HIGHLIGHT_CLASS); + }); + if (highlightClearTimer) { + clearTimeout(highlightClearTimer); + highlightClearTimer = null; + } + } + + function highlightClusterHit(el) { + if (!el) return; + clearClusterSearchHighlights(); + el.classList.add(HIGHLIGHT_CLASS); + highlightClearTimer = setTimeout(function () { + el.classList.remove(HIGHLIGHT_CLASS); + }, HIGHLIGHT_DURATION_MS); + } + + /** + * Scroll so el sits below the sticky stack (navbar + .clusters-controls search bar). + * Uses live layout after tab/panel updates (rAF). + */ + function scrollElementBelowStickyChrome(el) { + if (!el) return; + updateStickyLayoutMetrics(); + requestAnimationFrame(function () { + requestAnimationFrame(function () { + var margin = 14; + var chromeBottom; + if (controls) { + chromeBottom = Math.ceil(controls.getBoundingClientRect().bottom); + } else { + var navbar = document.getElementById('navbar-main'); + chromeBottom = navbar ? Math.ceil(navbar.getBoundingClientRect().bottom) : 72; + } + var elTopDoc = el.getBoundingClientRect().top + window.pageYOffset; + var targetScroll = elTopDoc - chromeBottom - margin; + window.scrollTo({ top: Math.max(0, targetScroll), behavior: 'smooth' }); + }); + }); + } - if (searchInput && searchResults) { + function hideSearchResults() { + if (searchToolbar) { + searchToolbar.innerHTML = ''; + searchToolbar.hidden = true; + } + if (searchResults) searchResults.innerHTML = ''; + if (searchPanel) searchPanel.classList.remove(RESULTS_OPEN_CLASS); + scheduleStickyLayoutMetrics(); + } + + function runInlineSearch() { + if (!searchInput || !searchResults || !searchPanel || !searchToolbar) return; + var tokens = tokenizeQuery(searchInput.value); + if (!tokens.length) { + hideSearchResults(); + return; + } + var results = collectClustersInlineSearchResults(root, tokens); + renderClustersInlineResults(results, searchToolbar, searchResults); + searchPanel.classList.add(RESULTS_OPEN_CLASS); + scheduleStickyLayoutMetrics(); + } + + if (searchInput && searchResults && searchPanel && searchToolbar) { searchInput.addEventListener('input', function () { clearTimeout(debounceTimer); - var query = this.value.toLowerCase().trim(); - if (query.length < 2) { - searchResults.style.display = 'none'; - searchResults.innerHTML = ''; - return; + debounceTimer = setTimeout(runInlineSearch, 200); + }); + + searchInput.addEventListener('keydown', function (e) { + if (e.key === 'Enter') { + e.preventDefault(); + clearTimeout(debounceTimer); + runInlineSearch(); } - debounceTimer = setTimeout(function () { - performClustersSearch(query, searchResults); - }, 200); }); - searchResults.addEventListener('click', function (e) { - var link = e.target.closest('.search-result-item'); + if (searchBtn) { + searchBtn.addEventListener('click', function () { + clearTimeout(debounceTimer); + runInlineSearch(); + searchInput.focus(); + }); + } + + document.addEventListener('keydown', function (e) { + if (e.key !== 'Escape') return; + var open = searchPanel.classList.contains(RESULTS_OPEN_CLASS); + var focusedIn = searchRoot && searchRoot.contains(document.activeElement); + if (!open && !focusedIn) return; + hideSearchResults(); + if (focusedIn && searchInput) searchInput.blur(); + }); + + searchPanel.addEventListener('click', function (e) { + if (e.target.closest('.clusters-inline-search__close')) { + e.preventDefault(); + hideSearchResults(); + return; + } + var link = e.target.closest('.clusters-inline-search__hit'); if (!link) return; e.preventDefault(); - var targetId = link.getAttribute('data-target'); - var target = targetId ? document.getElementById(targetId) : null; - if (target) target.scrollIntoView({ behavior: 'smooth', block: 'start' }); + var hitType = link.getAttribute('data-hit-type') || ''; + var clusterId = link.getAttribute('data-cluster'); + var tabId = link.getAttribute('data-tab') || ''; + var paneId = link.getAttribute('data-pane') || ''; + var section = clusterId ? document.getElementById(clusterId) : null; + if (!section) return; + + if (tabId) { + var tab = document.getElementById(tabId); + showBootstrapTab(tab); + } + + setTimeout(function () { + var scrollEl = null; + if (hitType === 'cluster') { + scrollEl = + section.querySelector('.cluster-header') || + section.querySelector('.cluster-title') || + section; + } else if (hitType === 'subcluster' && paneId) { + var paneSc = document.getElementById(paneId); + scrollEl = paneSc ? paneSc.querySelector('.sc-heading') || paneSc : section; + } else { + scrollEl = section.querySelector('.cluster-header') || section.querySelector('.cluster-title') || section; + } + if (scrollEl) { + highlightClusterHit(scrollEl); + scrollElementBelowStickyChrome(scrollEl); + } + }, 320); + + hideSearchResults(); + closeClustersMobileSidebar(); }); + + document.addEventListener( + 'click', + function (e) { + if (!searchPanel.classList.contains(RESULTS_OPEN_CLASS)) return; + if (searchRoot && searchRoot.contains(e.target)) return; + hideSearchResults(); + }, + true + ); } if (backToTopBtn) { diff --git a/static/js/clusters-search.js b/static/js/clusters-search.js deleted file mode 100644 index 43b8fdac3b3..00000000000 --- a/static/js/clusters-search.js +++ /dev/null @@ -1,637 +0,0 @@ -/** - * Clusters Page Search Functionality - * Enables searching within Bootstrap tab content that would otherwise be hidden from Ctrl-F - */ -(function() { - 'use strict'; - - // Wait for DOM to be ready - if (document.readyState === 'loading') { - document.addEventListener('DOMContentLoaded', init); - } else { - init(); - } - - function init() { - // Only run on clusters page - if (!window.location.pathname.includes('/clusters')) { - return; - } - - createSearchInterface(); - setupSearchHandlers(); - } - - function createSearchInterface() { - // Create sidebar container - const sidebar = document.createElement('div'); - sidebar.id = 'clusterSearchSidebar'; - sidebar.className = 'cluster-search-sidebar'; - sidebar.innerHTML = ` - -
-
-

Search Clusters

- -
-
-
- -
- -
-
- -
-
-
- `; - - // Insert at beginning of body - document.body.insertBefore(sidebar, document.body.firstChild); - } - - function setupSearchHandlers() { - const searchInput = document.getElementById('clusterSearchInput'); - const searchBtn = document.getElementById('clusterSearchBtn'); - const clearBtn = document.getElementById('clusterClearBtn'); - const resultsDiv = document.getElementById('clusterSearchResults'); - const toggleBtn = document.getElementById('clusterSearchToggle'); - const closeBtn = document.getElementById('clusterSearchClose'); - const panel = document.getElementById('clusterSearchPanel'); - - if (!searchInput || !searchBtn || !clearBtn || !toggleBtn || !closeBtn || !panel) return; - - // Toggle sidebar - toggleBtn.addEventListener('click', function() { - panel.classList.toggle('open'); - if (panel.classList.contains('open')) { - searchInput.focus(); - } - }); - - // Close sidebar - closeBtn.addEventListener('click', function() { - panel.classList.remove('open'); - }); - - // Close on escape key - document.addEventListener('keydown', function(e) { - if (e.key === 'Escape' && panel.classList.contains('open')) { - panel.classList.remove('open'); - } - }); - - // Search on button click - searchBtn.addEventListener('click', performSearch); - - // Search on Enter key - searchInput.addEventListener('keypress', function(e) { - if (e.key === 'Enter') { - performSearch(); - } - }); - - // Live search as user types (debounced) - var debounceTimer; - searchInput.addEventListener('input', function() { - clearTimeout(debounceTimer); - debounceTimer = setTimeout(performSearch, 300); - }); - - // Clear search - clearBtn.addEventListener('click', function() { - searchInput.value = ''; - resultsDiv.innerHTML = ''; - clearBtn.style.display = 'none'; - removeAllHighlights(); - collapseAllTabs(); - }); - } - - function performSearch() { - const searchInput = document.getElementById('clusterSearchInput'); - const clearBtn = document.getElementById('clusterClearBtn'); - const resultsDiv = document.getElementById('clusterSearchResults'); - const query = searchInput.value.trim(); - - if (!query || query.length < 2) { - resultsDiv.innerHTML = query.length > 0 ? '
Please enter at least 2 characters to search.
' : ''; - clearBtn.style.display = 'none'; - removeAllHighlights(); - return; - } - - // Remove previous highlights - removeAllHighlights(); - - // Search through all tab content - const results = searchAllTabs(query); - - // Display results - displayResults(results, query); - - // Show clear button - clearBtn.style.display = 'inline-block'; - } - - function searchAllTabs(query) { - const results = []; - const queryLower = query.toLowerCase(); - - // Find all cluster sections - const clusterSections = document.querySelectorAll('section[id^="cluster"]'); - - clusterSections.forEach(function(section) { - // Use h1 to get the actual cluster title (h3 is "Description" in the content) - const clusterTitle = section.querySelector('h1, .home-section-title'); - const clusterName = clusterTitle ? clusterTitle.textContent.trim() : 'Unknown Cluster'; - - // Search cluster title - if (clusterName.toLowerCase().includes(queryLower)) { - var titleRegex = new RegExp('(' + escapeRegExp(query) + ')', 'gi'); - results.push({ - cluster: clusterName, - tab: 'Title', - tabId: null, - snippet: escapeHtml(clusterName).replace(titleRegex, '$1'), - section: section, - tabPane: null, - tabLink: null, - element: clusterTitle || section - }); - } - - // Search description content (blocks outside tab panes) - var allSectionBlocks = section.querySelectorAll('li, p, h2, h3, h4, h5, h6, blockquote'); - var descriptionBlocks = Array.from(allSectionBlocks).filter(function(block) { - return !block.closest('.tab-pane'); - }).filter(function(block) { - var parent = block.parentElement; - while (parent && parent !== section) { - if (parent.matches('li, p, blockquote') && !parent.closest('.tab-pane')) return false; - parent = parent.parentElement; - } - return true; - }); - - descriptionBlocks.forEach(function(block) { - var text = block.textContent || ''; - if (text.toLowerCase().includes(queryLower)) { - var snippetText = text.trim(); - if (snippetText.length > 200) { - snippetText = snippetText.substring(0, 200) + '...'; - } - var highlightRegex = new RegExp('(' + escapeRegExp(query) + ')', 'gi'); - var snippet = escapeHtml(snippetText).replace(highlightRegex, '$1'); - - results.push({ - cluster: clusterName, - tab: 'Description', - tabId: null, - snippet: snippet, - section: section, - tabPane: null, - tabLink: null, - element: block - }); - } - }); - - // Find all tab panes in this cluster - const tabPanes = section.querySelectorAll('.tab-pane'); - - tabPanes.forEach(function(tabPane) { - const tabId = tabPane.id; - - // Get tab label - const tabLink = section.querySelector('a[href="#' + tabId + '"]'); - const tabLabel = tabLink ? tabLink.textContent.trim() : tabId; - const tabLabelLower = tabLabel.toLowerCase(); - - // If the tab label itself matches, add a result for it - if (tabLabelLower.includes(queryLower)) { - var regex = new RegExp('(' + escapeRegExp(query) + ')', 'gi'); - results.push({ - cluster: clusterName, - tab: tabLabel, - tabId: tabId, - snippet: 'Tab: ' + tabLabel.replace(regex, '$1'), - section: section, - tabPane: tabPane, - tabLink: tabLink, - element: tabPane - }); - } - - // Search each block-level element individually for per-paragraph results - // Filter out nested blocks (e.g.

inside

  • ) to avoid duplicates - var allBlocks = tabPane.querySelectorAll('li, p, h2, h3, h4, h5, h6, blockquote'); - var blocks = Array.from(allBlocks).filter(function(block) { - var parent = block.parentElement; - while (parent && parent !== tabPane) { - if (parent.matches('li, p, blockquote')) return false; - parent = parent.parentElement; - } - return true; - }); - - blocks.forEach(function(block) { - var text = block.textContent || ''; - if (text.toLowerCase().includes(queryLower)) { - var snippetText = text.trim(); - if (snippetText.length > 200) { - snippetText = snippetText.substring(0, 200) + '...'; - } - var highlightRegex = new RegExp('(' + escapeRegExp(query) + ')', 'gi'); - var snippet = escapeHtml(snippetText).replace(highlightRegex, '$1'); - - results.push({ - cluster: clusterName, - tab: tabLabel, - tabId: tabId, - snippet: snippet, - section: section, - tabPane: tabPane, - tabLink: tabLink, - element: block - }); - } - }); - }); - }); - - return results; - } - - function escapeRegExp(string) { - return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); - } - - function displayResults(results, query) { - const resultsDiv = document.getElementById('clusterSearchResults'); - - if (results.length === 0) { - resultsDiv.innerHTML = '
    No results found for "' + escapeHtml(query) + '".
    '; - return; - } - - var html = '
    Found ' + results.length + ' result(s)
    '; - html += '
    '; - - results.forEach(function(result, index) { - html += '
    ' + - '
    ' + escapeHtml(result.tab) + '
    ' + - '
    ' + escapeHtml(result.cluster) + '
    ' + - '
    ' + result.snippet + '
    ' + - '
    '; - }); - - html += '
    '; - resultsDiv.innerHTML = html; - - // Add click handlers to results - var resultItems = resultsDiv.querySelectorAll('.search-result-item'); - resultItems.forEach(function(item) { - item.addEventListener('click', function() { - var index = parseInt(this.getAttribute('data-result-index')); - var result = results[index]; - if (!result) return; - - removeAllHighlights(); - if (result.tabLink) { - activateTab(result); - } - highlightMatches(result.tabPane || result.element, query); - - // Scroll to the specific element (paragraph/reference) - setTimeout(function() { - scrollToElement(result.element); - }, 100); - - // Mark as active - resultItems.forEach(function(r) { r.classList.remove('active'); }); - this.classList.add('active'); - // Auto-hide the search panel - document.getElementById('clusterSearchPanel').classList.remove('open'); - }); - }); - - // Auto-expand first result - if (results.length > 0) { - resultItems[0].classList.add('active'); - if (results[0].tabLink) { - activateTab(results[0]); - } - highlightMatches(results[0].tabPane || results[0].element, query); - } - } - - function escapeHtml(text) { - const div = document.createElement('div'); - div.textContent = text; - return div.innerHTML; - } - - function activateTab(result) { - // Collapse all tabs first - collapseAllTabs(); - - // Activate the target tab - if (result.tabLink) { - result.tabLink.click(); - } - } - - function collapseAllTabs() { - document.querySelectorAll('.tab-pane.show.active').forEach(function(pane) { - pane.classList.remove('show', 'active'); - }); - document.querySelectorAll('.nav-link.active').forEach(function(link) { - link.classList.remove('active'); - }); - } - - function scrollToElement(element) { - // Get navbar height to offset the scroll - const navbar = document.querySelector('.navbar-fixed-top, .fixed-top, nav.navbar'); - const navbarHeight = navbar ? navbar.offsetHeight : 70; - - // Calculate the position to scroll to - const elementPosition = element.getBoundingClientRect().top + window.pageYOffset; - const offsetPosition = elementPosition - navbarHeight - 20; // Extra 20px padding - - // Scroll to the calculated position - window.scrollTo({ - top: offsetPosition, - behavior: 'smooth' - }); - } - - function highlightMatches(tabPane, query) { - if (!tabPane) return; - - // Remove existing highlights first - removeHighlightsInElement(tabPane); - - // Use mark.js-like approach to highlight matches - const regex = new RegExp(`(${escapeRegExp(query)})`, 'gi'); - - // Get all text nodes - const walker = document.createTreeWalker( - tabPane, - NodeFilter.SHOW_TEXT, - null, - false - ); - - const textNodes = []; - let node; - while ((node = walker.nextNode())) { - // Skip if parent is already a mark - if (node.parentElement.tagName !== 'MARK') { - textNodes.push(node); - } - } - - textNodes.forEach(function(textNode) { - const text = textNode.textContent; - const testRegex = new RegExp(`(${escapeRegExp(query)})`, 'gi'); - if (testRegex.test(text)) { - const fragment = document.createDocumentFragment(); - const tempDiv = document.createElement('div'); - tempDiv.innerHTML = text.replace(regex, '$1'); - while (tempDiv.firstChild) { - fragment.appendChild(tempDiv.firstChild); - } - textNode.parentNode.replaceChild(fragment, textNode); - } - }); - } - - function removeAllHighlights() { - document.querySelectorAll('.cluster-highlight').forEach(function(mark) { - const parent = mark.parentNode; - parent.replaceChild(document.createTextNode(mark.textContent), mark); - parent.normalize(); - }); - } - - function removeHighlightsInElement(element) { - element.querySelectorAll('.cluster-highlight').forEach(function(mark) { - const parent = mark.parentNode; - parent.replaceChild(document.createTextNode(mark.textContent), mark); - parent.normalize(); - }); - } - - // Add CSS for sidebar and highlighting - const style = document.createElement('style'); - style.textContent = ` - /* Highlight styling */ - .cluster-highlight { - background-color: #ffeb3b; - padding: 2px 0; - font-weight: bold; - } - - /* Sidebar toggle button */ - .cluster-search-toggle { - position: fixed; - left: 0; - top: 200px; - background: #007bff; - color: white; - border: none; - border-radius: 0 5px 5px 0; - padding: 12px 15px; - cursor: pointer; - z-index: 1034; - box-shadow: 2px 2px 5px rgba(0,0,0,0.2); - font-size: 14px; - transition: background 0.3s; - } - - .cluster-search-toggle:hover { - background: #0056b3; - } - - .cluster-search-toggle i { - margin-right: 5px; - } - - /* Sidebar panel */ - .cluster-search-panel { - position: fixed; - left: -350px; - top: 70px; - width: 350px; - height: calc(100vh - 70px); - background: white; - box-shadow: 2px 0 10px rgba(0,0,0,0.1); - z-index: 1035; - transition: left 0.3s ease; - display: flex; - flex-direction: column; - overflow: hidden; - } - - .cluster-search-panel.open { - left: 0; - } - - /* Sidebar header */ - .cluster-search-header { - display: flex; - justify-content: space-between; - align-items: center; - padding: 15px 20px; - border-bottom: 1px solid #dee2e6; - background: #f8f9fa; - } - - .cluster-search-header h4 { - margin: 0; - font-size: 18px; - color: #333; - } - - .cluster-search-close { - background: none; - border: none; - font-size: 20px; - color: #666; - cursor: pointer; - padding: 5px; - line-height: 1; - } - - .cluster-search-close:hover { - color: #333; - } - - /* Sidebar body */ - .cluster-search-body { - padding: 20px; - flex: 1; - overflow-y: auto; - } - - /* Search results summary */ - .search-summary { - background: #e7f3ff; - padding: 10px; - border-radius: 5px; - margin-bottom: 15px; - font-size: 0.9rem; - color: #004085; - } - - /* Search results list */ - .search-results-list { - display: flex; - flex-direction: column; - gap: 10px; - } - - /* Individual search result */ - .search-result-item { - background: #f8f9fa; - border: 1px solid #dee2e6; - border-radius: 5px; - padding: 12px; - cursor: pointer; - transition: all 0.2s; - } - - .search-result-item:hover { - background: #e9ecef; - border-color: #007bff; - box-shadow: 0 2px 5px rgba(0,0,0,0.1); - } - - .search-result-item.active { - background: #e7f3ff; - border-color: #007bff; - box-shadow: inset 0 0 0 1px #007bff; - } - - .search-result-header { - display: flex; - justify-content: space-between; - align-items: center; - margin-bottom: 5px; - } - - .search-result-header strong { - font-size: 0.95rem; - color: #333; - flex: 1; - margin-right: 10px; - } - - .search-result-header .badge { - font-size: 0.75rem; - } - - .search-result-cluster { - font-size: 0.8rem; - color: #666; - margin-bottom: 8px; - } - - .search-result-snippet { - font-size: 0.8rem; - color: #555; - line-height: 1.4; - } - - .search-result-snippet mark { - background-color: #ffeb3b; - padding: 1px 2px; - font-weight: 600; - } - - /* Mobile responsive */ - @media (max-width: 768px) { - .cluster-search-panel { - width: 70%; - left: -70%; - } - - .cluster-search-panel.open { - left: 0; - } - - .cluster-search-toggle { - top: 170px; - font-size: 14px; - padding: 10px; - } - - .cluster-search-toggle-text { - display: none; - } - } - - /* Alert styling in sidebar */ - .cluster-search-body .alert { - font-size: 0.85rem; - padding: 8px 12px; - } - `; - document.head.appendChild(style); - -})(); From 476afadec72a9a1a4c6956f53947e61ed2884c31 Mon Sep 17 00:00:00 2001 From: richarddushime Date: Mon, 23 Mar 2026 22:03:24 +0100 Subject: [PATCH 06/11] jump to active when tab clicked of sub cluster --- static/js/clusters-page.js | 82 ++++++++++++++++++++++++++------------ 1 file changed, 57 insertions(+), 25 deletions(-) diff --git a/static/js/clusters-page.js b/static/js/clusters-page.js index 3483774f965..ed8154a3743 100644 --- a/static/js/clusters-page.js +++ b/static/js/clusters-page.js @@ -255,6 +255,44 @@ if (window.ResizeObserver && navbarEl) { new ResizeObserver(scheduleStickyLayoutMetrics).observe(navbarEl); } + + /** + * Scroll so el sits below the sticky stack (navbar + .clusters-controls search bar). + * Uses live layout after tab/panel updates (rAF). + */ + function scrollElementBelowStickyChrome(el) { + if (!el) return; + updateStickyLayoutMetrics(); + requestAnimationFrame(function () { + requestAnimationFrame(function () { + var margin = 14; + var chromeBottom; + if (controls) { + chromeBottom = Math.ceil(controls.getBoundingClientRect().bottom); + } else { + var navbar = document.getElementById('navbar-main'); + chromeBottom = navbar ? Math.ceil(navbar.getBoundingClientRect().bottom) : 72; + } + var elTopDoc = el.getBoundingClientRect().top + window.pageYOffset; + var targetScroll = elTopDoc - chromeBottom - margin; + window.scrollTo({ top: Math.max(0, targetScroll), behavior: 'smooth' }); + }); + }); + } + + /** Tab anchor is .nav-link with href="#pane-id" pointing at .tab-pane inside clusters layout. */ + function scrollToClusterTabPaneFromTrigger(tabAnchor) { + if (!tabAnchor) return; + var href = tabAnchor.getAttribute('href'); + if (!href || href.charAt(0) !== '#') return; + var pane = document.querySelector(href); + if (!pane || !root.contains(pane)) return; + var scrollTarget = pane.querySelector('.sc-heading') || pane.querySelector('.cluster-tab-content') || pane; + setTimeout(function () { + scrollElementBelowStickyChrome(scrollTarget); + }, 80); + } + if (mobileToggle && sidebar) { mobileToggle.addEventListener('click', function () { sidebar.classList.toggle('sidebar-open'); @@ -294,13 +332,31 @@ var tab = document.getElementById(tabId); showBootstrapTab(tab); setTimeout(function () { - section.scrollIntoView({ behavior: 'smooth', block: 'start' }); + scrollToClusterTabPaneFromTrigger(tab); }, 100); } closeClustersMobileSidebar(); }); }); + /* Clicking sub-cluster tabs: scroll so pane content clears sticky chrome */ + if (typeof window.jQuery !== 'undefined' && window.jQuery.fn.tab) { + window + .jQuery(root) + .on('shown.bs.tab', '.cluster-tabs a[data-toggle="tab"], .cluster-tabs a[data-bs-toggle="tab"]', function () { + scrollToClusterTabPaneFromTrigger(this); + }); + } else { + root.querySelectorAll('.cluster-tabs a.nav-link[data-toggle="tab"], .cluster-tabs a.nav-link[data-bs-toggle="tab"]').forEach(function (tabEl) { + tabEl.addEventListener('click', function () { + var self = this; + setTimeout(function () { + scrollToClusterTabPaneFromTrigger(self); + }, 200); + }); + }); + } + var searchInput = document.getElementById('clusters-inline-search-input'); var searchBtn = document.getElementById('clusters-inline-search-btn'); var searchPanel = document.getElementById('clusters-inline-search-panel'); @@ -329,30 +385,6 @@ }, HIGHLIGHT_DURATION_MS); } - /** - * Scroll so el sits below the sticky stack (navbar + .clusters-controls search bar). - * Uses live layout after tab/panel updates (rAF). - */ - function scrollElementBelowStickyChrome(el) { - if (!el) return; - updateStickyLayoutMetrics(); - requestAnimationFrame(function () { - requestAnimationFrame(function () { - var margin = 14; - var chromeBottom; - if (controls) { - chromeBottom = Math.ceil(controls.getBoundingClientRect().bottom); - } else { - var navbar = document.getElementById('navbar-main'); - chromeBottom = navbar ? Math.ceil(navbar.getBoundingClientRect().bottom) : 72; - } - var elTopDoc = el.getBoundingClientRect().top + window.pageYOffset; - var targetScroll = elTopDoc - chromeBottom - margin; - window.scrollTo({ top: Math.max(0, targetScroll), behavior: 'smooth' }); - }); - }); - } - function hideSearchResults() { if (searchToolbar) { searchToolbar.innerHTML = ''; From d328ce1b6c21628860e8d9e9f4cbeb1b46b4e385 Mon Sep 17 00:00:00 2001 From: richarddushime Date: Tue, 24 Mar 2026 00:45:59 +0100 Subject: [PATCH 07/11] SEO booster for clusters --- assets/scss/custom.scss | 331 ++++++++++++++++-- content/clusters/_index.md | 34 ++ content/clusters/cluster-1/index.md | 20 ++ content/clusters/cluster-10/index.md | 20 ++ content/clusters/cluster-11/index.md | 20 ++ content/clusters/cluster-2/index.md | 20 ++ content/clusters/cluster-3/index.md | 20 ++ content/clusters/cluster-4/index.md | 20 ++ content/clusters/cluster-5/index.md | 20 ++ content/clusters/cluster-6/index.md | 20 ++ content/clusters/cluster-7/index.md | 20 ++ content/clusters/cluster-8/index.md | 20 ++ content/clusters/cluster-9/index.md | 20 ++ content/clusters/index.md | 9 - layouts/404.html | 7 + layouts/clusters/cluster.html | 83 +++++ layouts/clusters/list.html | 5 +- layouts/clusters/single.html | 8 +- layouts/partials/clusters/all_clusters.html | 137 +------- .../partials/clusters/cluster_section.html | 75 ++++ .../partials/clusters/cluster_seo_jsonld.html | 27 ++ .../partials/clusters/clusters_controls.html | 21 ++ layouts/partials/clusters/seo_jsonld.html | 30 ++ layouts/partials/clusters/sidebar_nav.html | 39 +++ layouts/partials/custom_head.html | 4 + layouts/partials/site_head.html | 7 + scripts/generate_cluster_pages.py | 68 ++++ static/js/clusters-page.js | 151 +++++++- 28 files changed, 1082 insertions(+), 174 deletions(-) create mode 100644 content/clusters/_index.md create mode 100644 content/clusters/cluster-1/index.md create mode 100644 content/clusters/cluster-10/index.md create mode 100644 content/clusters/cluster-11/index.md create mode 100644 content/clusters/cluster-2/index.md create mode 100644 content/clusters/cluster-3/index.md create mode 100644 content/clusters/cluster-4/index.md create mode 100644 content/clusters/cluster-5/index.md create mode 100644 content/clusters/cluster-6/index.md create mode 100644 content/clusters/cluster-7/index.md create mode 100644 content/clusters/cluster-8/index.md create mode 100644 content/clusters/cluster-9/index.md delete mode 100644 content/clusters/index.md create mode 100644 layouts/clusters/cluster.html create mode 100644 layouts/partials/clusters/cluster_section.html create mode 100644 layouts/partials/clusters/cluster_seo_jsonld.html create mode 100644 layouts/partials/clusters/clusters_controls.html create mode 100644 layouts/partials/clusters/seo_jsonld.html create mode 100644 layouts/partials/clusters/sidebar_nav.html create mode 100644 layouts/partials/custom_head.html create mode 100644 scripts/generate_cluster_pages.py diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index 273fa701a32..794d7b5e3a9 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -107,7 +107,7 @@ ); max-height: calc(100vh - var(--clusters-sticky-offset) - 20px); overflow-y: auto; - padding: 0.75rem; + padding: 0 0.75rem 0.75rem; background: #f8f9fa; border: 1px solid #e9ecef; border-radius: 8px; @@ -119,14 +119,30 @@ top: 0; z-index: 2; background: #f8f9fa; - padding: 0.15rem 0.1rem 0.45rem; + padding: 0; border-bottom: 1px solid #e9ecef; font-size: 0.75rem; font-weight: 700; text-transform: uppercase; letter-spacing: 0.5px; color: #888; - margin-bottom: 0.5rem; + margin: 0; +} + +/* No air between section label and cluster list (hub + subpages) */ +.clusters-sidebar-inner #cluster-nav { + margin: 0; + padding: 0; +} + +/* First cluster row: remove top padding (main source of “gap” below header border) */ +.clusters-sidebar-inner #cluster-nav > .cluster-nav-group:first-child > .cluster-nav-heading { + padding-top: 0; +} + +.clusters-sidebar-inner #cluster-nav > .cluster-nav-group:first-child.cluster-nav-group--active { + padding-top: 0; + margin-top: 0; } .cluster-nav-heading { @@ -148,6 +164,30 @@ color: #111; } +/* Current cluster on /clusters/cluster-N/ (see active_cluster_number in sidebar_nav) */ +.cluster-nav-group--active { + margin: 0 -0.15rem 0.35rem; + padding: 0.25rem 0.2rem 0.3rem; + border-radius: 6px; + background: rgba(139, 0, 0, 0.07); + border: 1px solid rgba(139, 0, 0, 0.14); +} + +.cluster-nav-heading--active { + color: #5a0000 !important; + background: rgba(255, 255, 255, 0.72); + font-weight: 700; +} + +.cluster-nav-heading--active:hover { + background: rgba(255, 255, 255, 0.88); + color: #3d0000 !important; +} + +.cluster-nav-group--active .cluster-nav-subs .nav-link { + color: #444; +} + .cluster-nav-toggle { display: inline-block; width: 1em; @@ -201,23 +241,24 @@ } .cluster-title { - font-size: 1.15rem; - font-weight: 700; + font-size: 0.95rem; + font-weight: 600; margin-bottom: 0.1rem; display: flex; align-items: center; - gap: 0.4rem; + gap: 0.35rem; + line-height: 1.3; } .cluster-number { display: inline-flex; align-items: center; justify-content: center; - width: 1.6em; - height: 1.6em; + width: 1.45em; + height: 1.45em; border-radius: 50%; background: rgba(0,0,0,0.1); - font-size: 0.8em; + font-size: 0.75em; flex-shrink: 0; } @@ -233,6 +274,11 @@ margin-bottom: 0.75rem; } +/* Search bar sits under page title (universal-wrapper); spacing via .mb-3 on wrapper */ +.clusters-title-toolbar { + max-width: 100%; +} + /* ---- Inline clusters list search (toolbar; not Algolia/site search) ---- */ .clusters-inline-search { position: relative; @@ -368,6 +414,10 @@ color: #888; } +.clusters-cluster-lead { + max-width: 48rem; +} + /* ---- Sub-cluster tabs (chip style + border: same on desktop & mobile) ---- */ .cluster-tabs { flex-wrap: wrap; @@ -433,9 +483,10 @@ /* ---- Sub-cluster heading & description ---- */ .sc-heading { - font-size: 1.1rem; - font-weight: 700; - margin-bottom: 0.5rem; + font-size: 0.95rem; + font-weight: 600; + margin-bottom: 0.45rem; + line-height: 1.3; } .sc-description { @@ -490,7 +541,8 @@ @media (max-width: 991px) { /* Flush under sticky controls (no mb-3 gap) + drawer meets toggle bar */ - .clusters-layout .clusters-controls { + .clusters-layout .clusters-controls, + .clusters-title-toolbar .clusters-controls { margin-bottom: 0 !important; } @@ -552,9 +604,9 @@ top: 0; z-index: 1; background: #f8f9fa; - padding: 0.15rem 0.1rem 0.45rem; + padding: 0; border-bottom: 1px solid #e9ecef; - margin-bottom: 0.5rem; + margin: 0; } /* Narrow screens: sized tab cells (base styles = borders match desktop) */ @@ -619,7 +671,7 @@ } .cluster-title { - font-size: 0.98rem; + font-size: 0.86rem; line-height: 1.35; } @@ -670,12 +722,12 @@ } .cluster-title { - font-size: 0.92rem; + font-size: 0.8rem; } .cluster-number { - width: 1.45em; - height: 1.45em; + width: 1.35em; + height: 1.35em; } .cluster-stats { @@ -688,7 +740,7 @@ } .sc-heading { - font-size: 0.98rem; + font-size: 0.88rem; } } @@ -1618,6 +1670,245 @@ article.article:has(table) .article-container { border-bottom: 1px solid #e9ecef; } +/* ---- /clusters/cluster-N/ only: sticky title + search;
    scrolls (desktop) ---- */ +/* Sticky on __head-wrap (not inner) — more reliable on iOS/mobile. */ +/* --cluster-subpage-sticky-top on :root (JS). z-index < navbar 1030. */ +.clusters-cluster-subpage { + overflow: visible; +} + +/* Opaque band so scrolled content doesn’t show through; full viewport width (overrides .universal-wrapper 1000px cap). */ +.clusters-cluster-subpage__head-wrap.universal-wrapper { + position: -webkit-sticky; + position: sticky; + top: var(--cluster-subpage-sticky-top, 72px); + z-index: 1018; + overflow: visible; + width: 100%; + max-width: none; + /* Match site base background (foundation) so it blends into the page. */ + background: #fefdf6; + box-shadow: none; +} + +.clusters-cluster-subpage__head-inner { + /* Match site base background (foundation) so it blends into the page. */ + background: #fefdf6; + padding-bottom: 0; + display: flex; + flex-direction: column; + align-items: center; + text-align: center; +} + +/* Center breadcrumb title row + wrapped lines */ +.clusters-cluster-subpage__head-inner .clusters-heading-row__crumbs { + justify-content: center; +} + +.clusters-cluster-subpage__head-inner .clusters-heading-row__title.clusters-site-heading { + flex: 0 1 auto; + text-align: center; +} + +.clusters-cluster-subpage__head-inner .clusters-title-toolbar { + width: 100%; + max-width: 32rem; + display: flex; + flex-direction: column; + align-items: stretch; +} + +.clusters-cluster-subpage__head-inner .clusters-inline-search__row { + justify-content: center; +} + +.clusters-cluster-subpage__head-inner .clusters-mobile-toggle { + text-align: center; +} + +/* No “card” behind search on cluster subpages */ +.clusters-cluster-subpage .clusters-controls { + position: static; + top: auto; + z-index: auto; + width: 100%; + max-width: 32rem; + margin-left: auto; + margin-right: auto; + margin-bottom: 0.25rem !important; + padding: 0.35rem 0; + background: transparent !important; + border: none !important; + box-shadow: none !important; +} + +.clusters-cluster-subpage__display.clusters-display-section { + /* Same foundation bg as .clusters-cluster-subpage__head-wrap */ + background: #fefdf6; + padding-top: 0.25rem; + margin-top: 0; + border-top: none; +} + +@media (min-width: 992px) { + .clusters-cluster-subpage__display { + overflow: hidden; + padding-top: 0.15rem; + } + + .clusters-layout--cluster-subpage .clusters-cluster-subpage__row { + align-items: stretch; + max-height: calc(100vh - var(--cluster-subpage-head-reserved, 220px)); + min-height: 280px; + } + + .clusters-cluster-subpage__main-scroll { + overflow-x: hidden; + overflow-y: auto; + -webkit-overflow-scrolling: touch; + overscroll-behavior: contain; + max-height: calc(100vh - var(--cluster-subpage-head-reserved, 220px)); + min-height: 0; + padding-bottom: 2rem; + } + + .clusters-cluster-subpage .clusters-sidebar { + display: flex; + flex-direction: column; + min-height: 0; + max-height: calc(100vh - var(--cluster-subpage-head-reserved, 220px)); + overflow: hidden; + } + + .clusters-cluster-subpage .clusters-sidebar-inner { + position: static !important; + top: auto !important; + flex: 1 1 auto; + min-height: 0; + max-height: none; + overflow-y: auto; + -webkit-overflow-scrolling: touch; + } +} + +@media (max-width: 991.98px) { + .clusters-cluster-subpage__main-scroll { + max-height: none !important; + overflow-y: visible !important; + } + + /* Drawer drops below title/search bar instead of full-height sheet from old top */ + .clusters-cluster-subpage .clusters-sidebar.sidebar-open { + top: var(--cluster-subpage-drawer-top, 200px); + bottom: auto; + /* Sass min() shadows CSS min(); pass through as unquoted string for the compiler */ + max-height: #{"min(78vh, calc(100dvh - var(--cluster-subpage-drawer-top, 200px) - env(safe-area-inset-bottom, 0px) - 8px))"}; + border-radius: 0 0 10px 10px; + box-shadow: 0 10px 28px rgba(0, 0, 0, 0.18); + border-top: 1px solid #dee2e6; + z-index: 1024; + padding-bottom: 0.75rem; + } +} + +/* Hub + /clusters/cluster-N/ — smaller than default Academic article H1 */ +h1.clusters-site-heading { + font-size: 1.45rem; + font-weight: 700; + line-height: 1.28; + margin-bottom: 0.35rem; + letter-spacing: -0.015em; +} + +/* /clusters/ section index only — larger hero title (see layouts/clusters/single.html) */ +h1.clusters-site-heading.clusters-hub-page__title { + font-size: 2.35rem; + line-height: 1.18; + margin-bottom: 0.5rem; + letter-spacing: -0.02em; +} + +/* Per-cluster page: FORRT clusters / Cluster N: Name — one flow (wraps on narrow screens) */ +.clusters-heading-row__crumbs { + display: flex; + flex-wrap: wrap; + align-items: baseline; + gap: 0.35rem 0.5rem; + margin: 0; + padding: 0; + list-style: none; +} + +.clusters-heading-row__parent { + font-size: 1.45rem; + font-weight: 700; + line-height: 1.28; + letter-spacing: -0.015em; + color: #8b0000; + text-decoration: none; + flex-shrink: 0; +} + +.clusters-heading-row__parent:hover { + text-decoration: underline; + color: #5a0000; +} + +.clusters-heading-row__sep { + font-size: 1.45rem; + font-weight: 400; + line-height: 1.28; + color: #adb5bd; + flex-shrink: 0; + user-select: none; +} + +.clusters-heading-row__title.clusters-site-heading { + margin: 0; + padding: 0; + font-size: 1.45rem; + flex: 1 1 14rem; + min-width: 0; +} + +@media (max-width: 768px) { + h1.clusters-site-heading { + font-size: 1.28rem; + } + + h1.clusters-site-heading.clusters-hub-page__title { + font-size: 1.95rem; + line-height: 1.2; + } + + .clusters-heading-row__parent, + .clusters-heading-row__sep, + .clusters-heading-row__title.clusters-site-heading { + font-size: 1.28rem; + line-height: 1.3; + } +} + +@media (max-width: 576px) { + h1.clusters-site-heading { + font-size: 1.12rem; + line-height: 1.32; + } + + h1.clusters-site-heading.clusters-hub-page__title { + font-size: 1.65rem; + line-height: 1.22; + } + + .clusters-heading-row__parent, + .clusters-heading-row__sep, + .clusters-heading-row__title.clusters-site-heading { + font-size: 1.12rem; + line-height: 1.32; + } +} + .clusters-back-to-top { position: fixed; right: 1.25rem; diff --git a/content/clusters/_index.md b/content/clusters/_index.md new file mode 100644 index 00000000000..19756247601 --- /dev/null +++ b/content/clusters/_index.md @@ -0,0 +1,34 @@ ++++ +# FORRT Clusters — full taxonomy (SEO + landing) +# Use _index.md (not index.md) so Hugo treats /clusters/ as a section and builds /clusters/cluster-N/ pages. +type = "clusters" +layout = "single" +# `title` → , Open Graph (via sharing_title), JSON-LD — not the on-page H1 +title = "Open Science & Reproducible Research Clusters — FORRT Taxonomy" +# Visible page heading (short); reverse of pre-SEO "FORRT's Clusters" +heading_title = "FORRT's Clusters" + +# Used in <meta name="description"> and Open Graph (Academic theme reads `summary` first) +summary = "Browse all 11 FORRT open science clusters in one page: replicability and the credibility revolution, FAIR data, transparency, pre-registration, meta-research, replication, qualitative open science, research integrity, and teaching resources. Interactive taxonomy with sub-clusters and curated references for educators and mentors." + +description = "Browse all 11 FORRT open science clusters in one page: replicability and the credibility revolution, FAIR data, transparency, pre-registration, meta-research, replication, qualitative open science, research integrity, and teaching resources. Interactive taxonomy with sub-clusters and curated references for educators and mentors." + +# Match `title` so og:title is the full SEO phrase (not shortened) +sharing_title = "Open Science & Reproducible Research Clusters — FORRT Taxonomy" +sharing_description = "All 11 FORRT clusters: open and reproducible science for teaching—replicability, FAIR data, transparency, meta-research, research integrity, and more, with sub-clusters and references." + +# Page bundle image → og:image, twitter previews, etc. (see site_head sharing_image_resource) +sharing_image_resource = "FORRT_Clusters.webp" +sharing_image_alt = "Diagram of FORRT's eleven open science clusters taxonomy" + +keywords = [ "open science clusters", "reproducible research", "FORRT taxonomy", "replicability", "open scholarship", "research transparency", "FAIR data", "meta-research", "research integrity", "teaching open science" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.9 ++++ + +Teaching Open and Reproducible Science shouldn't require educators to spend months sifting through a decade of literature. FORRT simplifies this process by providing a curated, expert-backed framework. Developed by over 50 scholars, our taxonomy organizes open scholarship into 11 distinct clusters, offering a clear pathway for integrating these tenets into your teaching and mentoring, regardless of your field or level of expertise. diff --git a/content/clusters/cluster-1/index.md b/content/clusters/cluster-1/index.md new file mode 100644 index 00000000000..410a46fd482 --- /dev/null +++ b/content/clusters/cluster-1/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 1 +title = "Cluster 1: Replication Crisis and Credibility Revolution — FORRT Open Science Taxonomy" +heading_title = "Cluster 1: Replication Crisis and Credibility Revolution" +summary = "FORRT Cluster 1: Replication Crisis and Credibility Revolution. Attainment of foundational knowledge on the importance of reproducible and open research (i.e., grounding the motivations and theoretical underpinnings of Open and Reproducible Science). Integration with field specific content (i.e.,…" +description = "FORRT Cluster 1: Replication Crisis and Credibility Revolution. Attainment of foundational knowledge on the importance of reproducible and open research (i.e., grounding the motivations and theoretical underpinnings of Open and Reproducible Science). Integration with field specific content (i.e.,…" +sharing_title = "Cluster 1: Replication Crisis and Credibility Revolution — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 1: Replication Crisis and Credibility Revolution. Attainment of foundational knowledge on the importance of reproducible and open research (i.e., grounding the motivations and theoretical underpinnings of Open and Reproducible Science). Integration with field specific content (i.e.,…" + +keywords = [ "FORRT cluster 1", "open science", "reproducible research", "Replication Crisis and Credibility Revolution" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-10/index.md b/content/clusters/cluster-10/index.md new file mode 100644 index 00000000000..accb07582b2 --- /dev/null +++ b/content/clusters/cluster-10/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 10 +title = "Cluster 10: Qualitative Research — FORRT Open Science Taxonomy" +heading_title = "Cluster 10: Qualitative Research" +summary = "FORRT Cluster 10: Qualitative Research. Invite review of: Qualitative Open Science OS Booklet.pdf Description Qualitative research refers to research conducted with non-numeric data, such as interviews, focus groups, ethnographies, photovoice, and others. There are 10 sub-clusters that can help read" +description = "FORRT Cluster 10: Qualitative Research. Invite review of: Qualitative Open Science OS Booklet.pdf Description Qualitative research refers to research conducted with non-numeric data, such as interviews, focus groups, ethnographies, photovoice, and others. There are 10 sub-clusters that can help read" +sharing_title = "Cluster 10: Qualitative Research — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 10: Qualitative Research. Invite review of: Qualitative Open Science OS Booklet.pdf Description Qualitative research refers to research conducted with non-numeric data, such as interviews, focus groups, ethnographies, photovoice, and others. There are 10 sub-clusters that can help read" + +keywords = [ "FORRT cluster 10", "open science", "reproducible research", "Qualitative Research" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-11/index.md b/content/clusters/cluster-11/index.md new file mode 100644 index 00000000000..130ab2e3d63 --- /dev/null +++ b/content/clusters/cluster-11/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 11 +title = "Cluster 11: Research Integrity — FORRT Open Science Taxonomy" +heading_title = "Cluster 11: Research Integrity" +summary = "FORRT Cluster 11: Research Integrity. Research Integrity (RI) encompasses the moral and professional standards that ensure research is trustworthy, transparent, and ethical from inception to publication​. Traditionally, RI efforts have centered on preventing misconduct—the blatant fabrication, fal" +description = "FORRT Cluster 11: Research Integrity. Research Integrity (RI) encompasses the moral and professional standards that ensure research is trustworthy, transparent, and ethical from inception to publication​. Traditionally, RI efforts have centered on preventing misconduct—the blatant fabrication, fal" +sharing_title = "Cluster 11: Research Integrity — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 11: Research Integrity. Research Integrity (RI) encompasses the moral and professional standards that ensure research is trustworthy, transparent, and ethical from inception to publication​. Traditionally, RI efforts have centered on preventing misconduct—the blatant fabrication, fal" + +keywords = [ "FORRT cluster 11", "open science", "reproducible research", "Research Integrity" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-2/index.md b/content/clusters/cluster-2/index.md new file mode 100644 index 00000000000..d826f9fbe46 --- /dev/null +++ b/content/clusters/cluster-2/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 2 +title = "Cluster 2: Conceptual and Statistical Knowledge — FORRT Open Science Taxonomy" +heading_title = "Conceptual and Statistical Knowledge" +summary = "FORRT Cluster 2: Conceptual and Statistical Knowledge. Attainment of a grounding in fundamental statistics, measurement, and its implications encompassing conceptual knowledge, application, interpretation and communication of statistical analyses. There are 8 sub-clusters which aim to further par…" +description = "FORRT Cluster 2: Conceptual and Statistical Knowledge. Attainment of a grounding in fundamental statistics, measurement, and its implications encompassing conceptual knowledge, application, interpretation and communication of statistical analyses. There are 8 sub-clusters which aim to further par…" +sharing_title = "Cluster 2: Conceptual and Statistical Knowledge — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 2: Conceptual and Statistical Knowledge. Attainment of a grounding in fundamental statistics, measurement, and its implications encompassing conceptual knowledge, application, interpretation and communication of statistical analyses. There are 8 sub-clusters which aim to further par…" + +keywords = [ "FORRT cluster 2", "open science", "reproducible research", "Conceptual and Statistical Knowledge" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-3/index.md b/content/clusters/cluster-3/index.md new file mode 100644 index 00000000000..8074875287a --- /dev/null +++ b/content/clusters/cluster-3/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 3 +title = "Cluster 3: Ways of Working — FORRT Open Science Taxonomy" +heading_title = "Cluster 3: Ways of Working" +summary = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:" +description = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:" +sharing_title = "Cluster 3: Ways of Working — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:" + +keywords = [ "FORRT cluster 3", "open science", "reproducible research", "Ways of Working" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-4/index.md b/content/clusters/cluster-4/index.md new file mode 100644 index 00000000000..acdf8e2dc85 --- /dev/null +++ b/content/clusters/cluster-4/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 4 +title = "Cluster 4: Pre-analysis Planning — FORRT Open Science Taxonomy" +heading_title = "Cluster 4: Pre-analysis Planning" +summary = "FORRT Cluster 4: Pre-analysis Planning. Pre-analysis planning entails laying out a complete methodology and analysis before a study has been undertaken. This facilitates transparency and removes several potential QRPs. When teaching, students should attain knowledge regarding what a pre-registration" +description = "FORRT Cluster 4: Pre-analysis Planning. Pre-analysis planning entails laying out a complete methodology and analysis before a study has been undertaken. This facilitates transparency and removes several potential QRPs. When teaching, students should attain knowledge regarding what a pre-registration" +sharing_title = "Cluster 4: Pre-analysis Planning — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 4: Pre-analysis Planning. Pre-analysis planning entails laying out a complete methodology and analysis before a study has been undertaken. This facilitates transparency and removes several potential QRPs. When teaching, students should attain knowledge regarding what a pre-registration" + +keywords = [ "FORRT cluster 4", "open science", "reproducible research", "Pre-analysis Planning" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-5/index.md b/content/clusters/cluster-5/index.md new file mode 100644 index 00000000000..5f1baadfe83 --- /dev/null +++ b/content/clusters/cluster-5/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 5 +title = "Cluster 5: Transparency and reproducibility in computation and analysis — FORRT Open Science Taxonomy" +heading_title = "Cluster 5: Transparency and reproducibility in computation and analysis" +summary = "FORRT Cluster 5: Transparency and reproducibility in computation and analysis. Attainment of the how-to basics of reproducible reports and analyses. It requires students to move towards transparent and scripted analysis practices in quantitative research. There are 5 sub-clusters which aim to fur…" +description = "FORRT Cluster 5: Transparency and reproducibility in computation and analysis. Attainment of the how-to basics of reproducible reports and analyses. It requires students to move towards transparent and scripted analysis practices in quantitative research. There are 5 sub-clusters which aim to fur…" +sharing_title = "Cluster 5: Transparency and reproducibility in computation and analysis — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 5: Transparency and reproducibility in computation and analysis. Attainment of the how-to basics of reproducible reports and analyses. It requires students to move towards transparent and scripted analysis practices in quantitative research. There are 5 sub-clusters which aim to fur…" + +keywords = [ "FORRT cluster 5", "open science", "reproducible research", "Transparency and reproducibility in computation and analysis" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-6/index.md b/content/clusters/cluster-6/index.md new file mode 100644 index 00000000000..82d44e1a80b --- /dev/null +++ b/content/clusters/cluster-6/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 6 +title = "Cluster 6: FAIR data and materials — FORRT Open Science Taxonomy" +heading_title = "Cluster 6: FAIR data and materials" +summary = "FORRT Cluster 6: FAIR data and materials. Students will learn about FAIR data (and education/research materials) principles that address Findability, Accessibility, Interoperability, and Reusability; engage with reasons to share data, the initiatives designed to increase scientific openness; as w…" +description = "FORRT Cluster 6: FAIR data and materials. Students will learn about FAIR data (and education/research materials) principles that address Findability, Accessibility, Interoperability, and Reusability; engage with reasons to share data, the initiatives designed to increase scientific openness; as w…" +sharing_title = "Cluster 6: FAIR data and materials — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 6: FAIR data and materials. Students will learn about FAIR data (and education/research materials) principles that address Findability, Accessibility, Interoperability, and Reusability; engage with reasons to share data, the initiatives designed to increase scientific openness; as w…" + +keywords = [ "FORRT cluster 6", "open science", "reproducible research", "FAIR data and materials" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-7/index.md b/content/clusters/cluster-7/index.md new file mode 100644 index 00000000000..65a145567ae --- /dev/null +++ b/content/clusters/cluster-7/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 7 +title = "Cluster 7: Publication Sharing — FORRT Open Science Taxonomy" +heading_title = "Cluster 7: Publication Sharing" +summary = "FORRT Cluster 7: Publication Sharing. This cluster has 6 sub-clusters:" +description = "FORRT Cluster 7: Publication Sharing. This cluster has 6 sub-clusters:" +sharing_title = "Cluster 7: Publication Sharing — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 7: Publication Sharing. This cluster has 6 sub-clusters:" + +keywords = [ "FORRT cluster 7", "open science", "reproducible research", "Publication Sharing" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-8/index.md b/content/clusters/cluster-8/index.md new file mode 100644 index 00000000000..c776d968051 --- /dev/null +++ b/content/clusters/cluster-8/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 8 +title = "Cluster 8: Replication and meta-research — FORRT Open Science Taxonomy" +heading_title = "Cluster 8: Replication and meta-research" +summary = "FORRT Cluster 8: Replication and meta-research. Attainment of a grounding in 'replication research', which takes a variety of forms, each with a different purpose and contribution. Replicable science requires replication research. When teaching, students should understand the purpose and need of …" +description = "FORRT Cluster 8: Replication and meta-research. Attainment of a grounding in 'replication research', which takes a variety of forms, each with a different purpose and contribution. Replicable science requires replication research. When teaching, students should understand the purpose and need of …" +sharing_title = "Cluster 8: Replication and meta-research — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 8: Replication and meta-research. Attainment of a grounding in 'replication research', which takes a variety of forms, each with a different purpose and contribution. Replicable science requires replication research. When teaching, students should understand the purpose and need of …" + +keywords = [ "FORRT cluster 8", "open science", "reproducible research", "Replication and meta-research" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/cluster-9/index.md b/content/clusters/cluster-9/index.md new file mode 100644 index 00000000000..c7f750b10c9 --- /dev/null +++ b/content/clusters/cluster-9/index.md @@ -0,0 +1,20 @@ ++++ +type = "clusters" +layout = "cluster" +cluster_number = 9 +title = "Cluster 9: Academic Structures and Institutions — FORRT Open Science Taxonomy" +heading_title = "Cluster 9: Academic Structures and Institutions" +summary = "FORRT Cluster 9: Academic Structures and Institutions. Attainment of a grounding in topics related to academia and academics. Students should understand how individuals, teams, institutions, and academic culture work together to promote (or hinder) openness, inclusion, diversity, equity, and tran…" +description = "FORRT Cluster 9: Academic Structures and Institutions. Attainment of a grounding in topics related to academia and academics. Students should understand how individuals, teams, institutions, and academic culture work together to promote (or hinder) openness, inclusion, diversity, equity, and tran…" +sharing_title = "Cluster 9: Academic Structures and Institutions — FORRT Open Science Taxonomy" +sharing_description = "FORRT Cluster 9: Academic Structures and Institutions. Attainment of a grounding in topics related to academia and academics. Students should understand how individuals, teams, institutions, and academic culture work together to promote (or hinder) openness, inclusion, diversity, equity, and tran…" + +keywords = [ "FORRT cluster 9", "open science", "reproducible research", "Academic Structures and Institutions" ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ diff --git a/content/clusters/index.md b/content/clusters/index.md deleted file mode 100644 index b10dbfa04b0..00000000000 --- a/content/clusters/index.md +++ /dev/null @@ -1,9 +0,0 @@ -+++ -# FORRT Clusters -title = "FORRT's Clusters" -description = "Comprehensive taxonomy of Open and Reproducible Science concepts with 11 interconnected clusters" - -# Optional metadata -date = 2024-01-01 -draft = false -+++ diff --git a/layouts/404.html b/layouts/404.html index ebadbcfe30f..3e691d1c470 100644 --- a/layouts/404.html +++ b/layouts/404.html @@ -24,6 +24,12 @@ return; } + // Old taxonomy index URL (resource tag list root) → main clusters taxonomy page + if (/^\/forrt_clusters\/?$/i.test(path)) { + window.location.replace('/clusters/'); + return; + } + var redirects = [ { pattern: /^\/curated_resources(\/|$)/, target: '/resources/' }, { pattern: /^\/glossary\/([^/]+)\/.+/, target: '/glossary/$1/' }, @@ -70,6 +76,7 @@ <h3>Here are some useful links:</h3> <li><a href="{{ .Site.BaseURL }}replication-hub/">Replication Hub</a></li> <li><a href="{{ .Site.BaseURL }}lesson-plans/">Lesson Plans</a></li> <li><a href="{{ .Site.BaseURL }}publications/">Publications</a></li> + <li><a href="{{ .Site.BaseURL }}clusters/"> FORRT's Clusters</a></li> </ul> </div> diff --git a/layouts/clusters/cluster.html b/layouts/clusters/cluster.html new file mode 100644 index 00000000000..3ded15724b6 --- /dev/null +++ b/layouts/clusters/cluster.html @@ -0,0 +1,83 @@ +{{/* + Per-cluster URLs (/clusters/cluster-N/) — SEO rationale + + Each cluster is a first-class page with its own canonical URL, crawlable HTML, and + front-matter–driven <title>, meta description, and Open Graph/Twitter fields. That gives + search engines one clear, indexable document per topic (the cluster and its sub-clusters) + instead of relying on hash fragments or a single long hub page for all eleven. + + Structured data (JSON-LD via cluster_seo_jsonld) can describe the page and taxonomy entity + in context, improving machine-readable signals for that URL. + + The hub (/clusters/) remains the overview and entry point; these pages are satellites in a + classic topic-cluster model—internal links between hub and subpages distribute relevance + and help users and crawlers discover each cluster explicitly. + + Shareable links resolve to stable URLs with focused headings, which supports accurate + snippets, social previews, and external citations to the right slice of the taxonomy. +*/}} +{{ define "main" }} +{{ $n := int .Params.cluster_number }} +{{ $data := site.Data.clusters_v4 }} +{{ $cluster := false }} +{{ if $data }} + {{ range $data.clusters }} + {{ if eq (int .number) $n }}{{ $cluster = . }}{{ end }} + {{ end }} +{{ end }} + +{{ if not $cluster }} + <div class="universal-wrapper pt-3 pb-3"> + <div class="container"> + <p class="alert alert-warning">Cluster data not found. <a href="{{ "/clusters/" | relURL }}">Back to all clusters</a>.</p> + </div> + </div> +{{ else }} + {{ partial "clusters/cluster_seo_jsonld.html" (dict "page" . "cluster" $cluster) }} + + <div class="clusters-cluster-subpage"> + <div class="universal-wrapper pt-2 pb-0 clusters-cluster-subpage__head-wrap"> + <div class="container"> + <div class="clusters-cluster-subpage__head-inner"> + {{ $heading := .Params.heading_title | default .Title }} + <nav aria-label="breadcrumb" class="clusters-heading-row__crumbs mb-1"> + <a href="{{ "/clusters/" | relURL }}" class="clusters-heading-row__parent">FORRT clusters</a> + <span class="clusters-heading-row__sep" aria-hidden="true">/</span> + <h1 class="clusters-heading-row__title clusters-site-heading" itemprop="headline">{{ $heading }}</h1> + </nav> + + <div class="clusters-title-toolbar"> + {{ partial "clusters/clusters_controls.html" . }} + </div> + </div> + </div> + </div> + + {{ $colors := slice "#cacfdc" "#eadce6" "#d4e4d9" "#BDC5CA" "#dce4ea" "#e8ddd4" "#c9dbcb" "#d9cfe0" "#cddde3" "#e0d8cc" "#d4dce8" }} + {{ $arrowColors := slice "#6070a0" "#a05080" "#408060" "#607080" "#5080a0" "#a08060" "#509060" "#8060a0" "#5090a0" "#907050" "#6070a0" }} + {{ $ci := sub $n 1 }} + + <section class="clusters-display-section clusters-cluster-subpage__display"> + <div class="container"> + <div class="clusters-layout clusters-layout--cluster-subpage"> + <div class="row clusters-cluster-subpage__row"> + {{ partial "clusters/sidebar_nav.html" (dict "data" $data "arrowColors" $arrowColors "link_mode" "subpath" "active_cluster_number" $n) }} + <main class="col-12 col-lg-8 col-xl-9 clusters-content clusters-cluster-subpage__main-scroll"> + {{ with .Content }} + <div class="article-container pt-2 pb-2"> + <div class="article-style clusters-cluster-lead">{{ . }}</div> + </div> + {{ end }} + {{ partial "clusters/cluster_section.html" (dict "cluster" $cluster "ci" $ci "colors" $colors) }} + </main> + </div> + </div> + + <button type="button" class="clusters-back-to-top" id="clusters-back-to-top" aria-label="Back to top"> + <i class="fas fa-arrow-up" aria-hidden="true"></i> + </button> + </div> + </section> + </div> +{{ end }} +{{ end }} diff --git a/layouts/clusters/list.html b/layouts/clusters/list.html index 5ebc8e911f4..2c31da27d70 100644 --- a/layouts/clusters/list.html +++ b/layouts/clusters/list.html @@ -1,17 +1,18 @@ {{/* layouts/clusters/list.html - List layout for clusters section */}} {{ define "main" }} + {{ partial "clusters/seo_jsonld.html" . }} <div class="universal-wrapper pt-3 pb-3"> <div class="container"> {{/* Clusters page header */}} {{ if .Params.image }} <div class="article-header d-print-none"> - <img src="{{ .Params.image }}" alt="{{ .Title }}" class="article-banner" loading="lazy"> + <img src="{{ .Params.image }}" alt="{{ .Params.heading_title | default .Title }}" class="article-banner" loading="lazy"> </div> {{ end }} <div class="article-container pt-3"> - <h1 itemprop="headline">{{ .Title }}</h1> + <h1 class="clusters-site-heading" itemprop="headline">{{ .Params.heading_title | default .Title }}</h1> {{/* Subtitle if present */}} {{ if .Params.subtitle }} diff --git a/layouts/clusters/single.html b/layouts/clusters/single.html index 5dae5ade492..7c2e3be0953 100644 --- a/layouts/clusters/single.html +++ b/layouts/clusters/single.html @@ -1,17 +1,19 @@ -{{/* layouts/clusters/single.html - Main layout for clusters page */}} +{{/* layouts/clusters/single.html - Main layout for clusters page (same H1/SEO split as list.html) */}} {{ define "main" }} + {{ partial "clusters/seo_jsonld.html" . }} <div class="universal-wrapper pt-3 pb-3"> <div class="container"> {{/* Clusters page header */}} {{ if .Params.image }} <div class="article-header d-print-none"> - <img src="{{ .Params.image }}" alt="{{ .Title }}" class="article-banner" loading="lazy"> + <img src="{{ .Params.image }}" alt="{{ .Params.heading_title | default .Title }}" class="article-banner" loading="lazy"> </div> {{ end }} <div class="article-container pt-3"> - <h1 itemprop="headline">{{ .Title }}</h1> + {{/* Hub /clusters/ only: larger H1 (cluster subpages use layout cluster, not this template) */}} + <h1 class="clusters-site-heading{{ if and .IsNode (eq .Section "clusters") }} clusters-hub-page__title{{ end }}" itemprop="headline">{{ .Params.heading_title | default .Title }}</h1> {{/* Subtitle if present */}} {{ if .Params.subtitle }} diff --git a/layouts/partials/clusters/all_clusters.html b/layouts/partials/clusters/all_clusters.html index 0fe9ee2599a..5f2a1c8a793 100644 --- a/layouts/partials/clusters/all_clusters.html +++ b/layouts/partials/clusters/all_clusters.html @@ -12,141 +12,16 @@ <div class="clusters-layout"> - <div class="clusters-controls mb-3"> - {{/* Inline cluster list search (not site search; JS: static/js/clusters-page.js) */}} - <div class="clusters-inline-search"> - <div class="clusters-inline-search__row"> - <input type="text" id="clusters-inline-search-input" class="form-control clusters-inline-search__input" - placeholder="Search clusters…" aria-label="Search clusters and sub-clusters" autocomplete="off" spellcheck="false"> - <button type="button" class="btn btn-sm btn-primary clusters-inline-search__submit" id="clusters-inline-search-btn" aria-label="Run search"> - <i class="fas fa-search" aria-hidden="true"></i> - </button> - </div> - <div id="clusters-inline-search-panel" class="clusters-inline-search__panel"> - <div id="clusters-inline-search-toolbar" class="clusters-inline-search__toolbar-host" hidden></div> - <div id="clusters-inline-search-results" class="clusters-inline-search__results-body" aria-live="polite"></div> - </div> - </div> - - {{/* ===== MOBILE NAV TOGGLE ===== */}} - <button class="btn btn-sm btn-outline-secondary d-lg-none clusters-mobile-toggle" type="button" - id="clusters-mobile-toggle"> - ☰ Navigate clusters - </button> - </div> + {{ partial "clusters/clusters_controls.html" . }} <div class="row"> - {{/* ===== SIDEBAR ===== */}} - <div class="col-lg-4 col-xl-3 clusters-sidebar" id="clusters-sidebar"> - <div class="clusters-sidebar-inner"> - <div class="sidebar-header">Clusters & Sub-clusters</div> - <nav id="cluster-nav"> - {{ range $ci, $cluster := $data.clusters }} - {{ $cid := printf "cluster-%d" (int $cluster.number) }} - <div class="cluster-nav-group" data-cluster="{{ $cid }}"> - <a href="#{{ $cid }}" class="cluster-nav-heading"> - {{ $arrowColor := index $arrowColors (mod $ci (len $arrowColors)) }} - <span class="cluster-nav-toggle" style="color:{{ $arrowColor }};">▸</span> - {{ $cluster.name }} - </a> - <ul class="cluster-nav-subs" style="display:none;"> - {{ range $si, $sc := $cluster.sub_clusters }} - {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} - <li class="nav-item"> - <a href="#{{ $cid }}" class="nav-link sc-nav-link" data-cluster="{{ $cid }}" data-tab="{{ $scid }}-tab"> - {{ $sc.name }} - <span class="badge badge-pill">{{ len $sc.publications }}</span> - </a> - </li> - {{ end }} - </ul> - </div> - {{ end }} - </nav> - </div> - </div> - - {{/* ===== MAIN CONTENT ===== */}} - <main class="col-12 col-lg-8 col-xl-9 clusters-content"> - {{ range $ci, $cluster := $data.clusters }} - {{ $cid := printf "cluster-%d" (int $cluster.number) }} - {{ $color := index $colors (mod $ci (len $colors)) }} - {{ $totalPubs := 0 }}{{ range $cluster.sub_clusters }}{{ $totalPubs = add $totalPubs (len .publications) }}{{ end }} + {{ partial "clusters/sidebar_nav.html" (dict "data" $data "arrowColors" $arrowColors "link_mode" "anchor") }} - <section id="{{ $cid }}" class="cluster-section" style="background-color: {{ $color }};"> - <div class="cluster-header"> - <h2 class="cluster-title"> - <span class="cluster-number">{{ (int $cluster.number) }}</span> - {{ $cluster.name }} - </h2> - <span class="cluster-stats">{{ len $cluster.sub_clusters }} sub-clusters · {{ $totalPubs }} references</span> - </div> - - {{ if $cluster.description }} - <p class="cluster-description">{{ $cluster.description }}</p> + <main class="col-12 col-lg-8 col-xl-9 clusters-content"> + {{ range $ci, $cluster := $data.clusters }} + {{ partial "clusters/cluster_section.html" (dict "cluster" $cluster "ci" $ci "colors" $colors) }} {{ end }} - - {{/* Sub-cluster tabs */}} - {{ if gt (len $cluster.sub_clusters) 0 }} - <ul class="nav nav-tabs cluster-tabs" id="tabs-{{ $cid }}" role="tablist"> - {{ range $si, $sc := $cluster.sub_clusters }} - {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} - <li class="nav-item"> - <a class="nav-link{{ if eq $si 0 }} active{{ end }}" id="{{ $scid }}-tab" - data-toggle="tab" href="#{{ $scid }}" role="tab" - aria-controls="{{ $scid }}" aria-selected="{{ if eq $si 0 }}true{{ else }}false{{ end }}"> - {{ $sc.name }} - <span class="tab-count">{{ len $sc.publications }}</span> - </a> - </li> - {{ end }} - </ul> - - <div class="tab-content cluster-tab-content" id="content-{{ $cid }}"> - {{ range $si, $sc := $cluster.sub_clusters }} - {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} - <div class="tab-pane fade{{ if eq $si 0 }} show active{{ end }}" id="{{ $scid }}" - role="tabpanel" aria-labelledby="{{ $scid }}-tab"> - - <h3 class="sc-heading">{{ $sc.name }}</h3> - - {{ if $sc.description }} - <p class="sc-description">{{ $sc.description }}</p> - {{ end }} - - {{ if $sc.publications }} - <ul class="publication-list"> - {{ range $sc.publications }} - <li class="publication-item"> - {{ $ref := .apa }} - {{/* Strip DOI URL from text - we show it separately */}} - {{ $ref = replaceRE `\s*https?://(?:dx\.)?doi\.org/\S+` "" $ref }} - {{ $ref = replaceRE `\s+$` "" $ref }} - {{/* Strip dangerous tags but keep i/em for italics (data from doi.org is trusted) */}} - {{ $ref = replaceRE `<script[^>]*>.*?</script>` "" $ref }} - {{ $ref = replaceRE `<iframe[^>]*>.*?</iframe>` "" $ref }} - {{/* Linkify remaining URLs */}} - {{ $ref = replaceRE `(https?://\S+)` `<a href="$1" target="_blank" rel="noopener">$1</a>` $ref }} - {{ $ref | safeHTML }} - {{ if .doi }} - {{ $doiURL := printf "https://doi.org/%s" .doi }} - <a href="{{ $doiURL }}" target="_blank" rel="noopener">{{ $doiURL }}</a> - {{ end }} - </li> - {{ end }} - </ul> - {{ else }} - <p class="text-muted"><em>No publications listed for this sub-cluster yet.</em></p> - {{ end }} - - </div> - {{ end }} - </div> - {{ end }} - </section> - - {{ end }} - </main> + </main> </div> </div> diff --git a/layouts/partials/clusters/cluster_section.html b/layouts/partials/clusters/cluster_section.html new file mode 100644 index 00000000000..b62aecfb463 --- /dev/null +++ b/layouts/partials/clusters/cluster_section.html @@ -0,0 +1,75 @@ +{{/* One cluster block (used on /clusters/ and /clusters/cluster-N/). Expects dict: cluster, ci, colors */}} +{{ $cluster := .cluster }} +{{ $ci := .ci }} +{{ $colors := .colors }} +{{ $cid := printf "cluster-%d" (int $cluster.number) }} +{{ $color := index $colors (mod $ci (len $colors)) }} +{{ $totalPubs := 0 }}{{ range $cluster.sub_clusters }}{{ $totalPubs = add $totalPubs (len .publications) }}{{ end }} + +<section id="{{ $cid }}" class="cluster-section" style="background-color: {{ $color }};"> + <div class="cluster-header"> + <h2 class="cluster-title"> + <span class="cluster-number">{{ (int $cluster.number) }}</span> + {{ $cluster.name }} + </h2> + <span class="cluster-stats">{{ len $cluster.sub_clusters }} sub-clusters · {{ $totalPubs }} references</span> + </div> + + {{ if $cluster.description }} + <p class="cluster-description">{{ $cluster.description }}</p> + {{ end }} + + {{ if gt (len $cluster.sub_clusters) 0 }} + <ul class="nav nav-tabs cluster-tabs" id="tabs-{{ $cid }}" role="tablist"> + {{ range $si, $sc := $cluster.sub_clusters }} + {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} + <li class="nav-item"> + <a class="nav-link{{ if eq $si 0 }} active{{ end }}" id="{{ $scid }}-tab" + data-toggle="tab" href="#{{ $scid }}" role="tab" + aria-controls="{{ $scid }}" aria-selected="{{ if eq $si 0 }}true{{ else }}false{{ end }}"> + {{ $sc.name }} + <span class="tab-count">{{ len $sc.publications }}</span> + </a> + </li> + {{ end }} + </ul> + + <div class="tab-content cluster-tab-content" id="content-{{ $cid }}"> + {{ range $si, $sc := $cluster.sub_clusters }} + {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} + <div class="tab-pane fade{{ if eq $si 0 }} show active{{ end }}" id="{{ $scid }}" + role="tabpanel" aria-labelledby="{{ $scid }}-tab"> + + <h3 class="sc-heading">{{ $sc.name }}</h3> + + {{ if $sc.description }} + <p class="sc-description">{{ $sc.description }}</p> + {{ end }} + + {{ if $sc.publications }} + <ul class="publication-list"> + {{ range $sc.publications }} + <li class="publication-item"> + {{ $ref := .apa }} + {{ $ref = replaceRE `\s*https?://(?:dx\.)?doi\.org/\S+` "" $ref }} + {{ $ref = replaceRE `\s+$` "" $ref }} + {{ $ref = replaceRE `<script[^>]*>.*?</script>` "" $ref }} + {{ $ref = replaceRE `<iframe[^>]*>.*?</iframe>` "" $ref }} + {{ $ref = replaceRE `(https?://\S+)` `<a href="$1" target="_blank" rel="noopener">$1</a>` $ref }} + {{ $ref | safeHTML }} + {{ if .doi }} + {{ $doiURL := printf "https://doi.org/%s" .doi }} + <a href="{{ $doiURL }}" target="_blank" rel="noopener">{{ $doiURL }}</a> + {{ end }} + </li> + {{ end }} + </ul> + {{ else }} + <p class="text-muted"><em>No publications listed for this sub-cluster yet.</em></p> + {{ end }} + + </div> + {{ end }} + </div> + {{ end }} +</section> diff --git a/layouts/partials/clusters/cluster_seo_jsonld.html b/layouts/partials/clusters/cluster_seo_jsonld.html new file mode 100644 index 00000000000..4c7c779a478 --- /dev/null +++ b/layouts/partials/clusters/cluster_seo_jsonld.html @@ -0,0 +1,27 @@ +{{/* Structured data for a single cluster page. Expects dict: page, cluster */}} +{{ $p := .page }} +{{ $c := .cluster }} +{{ if not $c }}{{ return }}{{ end }} + +{{ $summary := $p.Params.summary | default $p.Description | default "" }} +{{ if eq $summary "" }} + {{ with $c.description }}{{ $summary = plainify . | truncate 300 "…" }}{{ end }} +{{ end }} +{{ if eq $summary "" }}{{ $summary = printf "FORRT Cluster %d: %s." (int $c.number) $c.name }}{{ end }} + +{{ $hubURL := "clusters/" | absURL }} + +{{ $webpage := dict "@type" "WebPage" "@id" (printf "%s#webpage" $p.Permalink) "url" $p.Permalink "name" $p.Title "description" $summary "inLanguage" (site.LanguageCode | default "en-US") }} +{{ if and $p.Params.sharing_image_resource ($p.Resources.GetMatch $p.Params.sharing_image_resource) }} + {{ $pimg := $p.Resources.GetMatch $p.Params.sharing_image_resource }} + {{ $webpage = merge $webpage (dict "primaryImageOfPage" (dict "@type" "ImageObject" "url" $pimg.Permalink)) }} +{{ end }} + +{{ $breadcrumb := dict "@type" "BreadcrumbList" "itemListElement" (slice + (dict "@type" "ListItem" "position" 1 "name" "FORRT Clusters" "item" $hubURL) + (dict "@type" "ListItem" "position" 2 "name" (printf "Cluster %d: %s" (int $c.number) $c.name) "item" $p.Permalink) +) }} + +{{ $graph := slice $webpage $breadcrumb }} +{{ $root := dict "@context" "https://schema.org" "@graph" $graph }} +<script type="application/ld+json">{{ $root | jsonify | safeHTML }}</script> diff --git a/layouts/partials/clusters/clusters_controls.html b/layouts/partials/clusters/clusters_controls.html new file mode 100644 index 00000000000..b6c34483b0d --- /dev/null +++ b/layouts/partials/clusters/clusters_controls.html @@ -0,0 +1,21 @@ +{{/* Search toolbar + mobile nav toggle (shared by hub and cluster subpages) */}} +<div class="clusters-controls mb-3"> + <div class="clusters-inline-search"> + <div class="clusters-inline-search__row"> + <input type="text" id="clusters-inline-search-input" class="form-control clusters-inline-search__input" + placeholder="Search clusters…" aria-label="Search clusters and sub-clusters" autocomplete="off" spellcheck="false"> + <button type="button" class="btn btn-sm btn-primary clusters-inline-search__submit" id="clusters-inline-search-btn" aria-label="Run search"> + <i class="fas fa-search" aria-hidden="true"></i> + </button> + </div> + <div id="clusters-inline-search-panel" class="clusters-inline-search__panel"> + <div id="clusters-inline-search-toolbar" class="clusters-inline-search__toolbar-host" hidden></div> + <div id="clusters-inline-search-results" class="clusters-inline-search__results-body" aria-live="polite"></div> + </div> + </div> + + <button class="btn btn-sm btn-outline-secondary d-lg-none clusters-mobile-toggle" type="button" + id="clusters-mobile-toggle"> + ☰ Navigate clusters and sub-clusters + </button> +</div> diff --git a/layouts/partials/clusters/seo_jsonld.html b/layouts/partials/clusters/seo_jsonld.html new file mode 100644 index 00000000000..31502129501 --- /dev/null +++ b/layouts/partials/clusters/seo_jsonld.html @@ -0,0 +1,30 @@ +{{/* Structured data: WebPage + ItemList of all clusters for search engines */}} +{{ $data := site.Data.clusters_v4 }} +{{ if not $data }}{{ return }}{{ end }} + +{{ $summary := .Params.summary | default .Description | default "" }} +{{ if eq $summary "" }} + {{ with .Summary }}{{ $summary = plainify . | truncate 300 "…" }}{{ end }} +{{ end }} +{{ if eq $summary "" }}{{ $summary = "FORRT open science clusters taxonomy for educators and researchers." }}{{ end }} + +{{ $elements := slice }} +{{ range $i, $c := $data.clusters }} + {{ $d := "" }} + {{ with $c.description }}{{ $d = plainify . | truncate 240 "…" }}{{ end }} + {{ $itemURL := printf "clusters/cluster-%d/" (int $c.number) | absURL }} + {{ $wp := dict "@type" "WebPage" "name" $c.name "url" $itemURL }} + {{ if $d }}{{ $wp = merge $wp (dict "description" $d) }}{{ end }} + {{ $item := dict "@type" "ListItem" "position" (add $i 1) "item" $wp }} + {{ $elements = $elements | append $item }} +{{ end }} + +{{ $webpage := dict "@type" "WebPage" "@id" (printf "%s#webpage" .Permalink) "url" .Permalink "name" .Title "description" $summary "inLanguage" (site.LanguageCode | default "en-US") }} +{{ if and .Params.sharing_image_resource (.Resources.GetMatch .Params.sharing_image_resource) }} + {{ $pimg := .Resources.GetMatch .Params.sharing_image_resource }} + {{ $webpage = merge $webpage (dict "primaryImageOfPage" (dict "@type" "ImageObject" "url" $pimg.Permalink)) }} +{{ end }} +{{ $itemlist := dict "@type" "ItemList" "@id" (printf "%s#itemlist" .Permalink) "name" "FORRT Open Science Clusters" "description" "Full taxonomy of open and reproducible science clusters with sub-clusters and teaching references." "numberOfItems" (len $data.clusters) "itemListElement" $elements }} +{{ $graph := slice $webpage $itemlist }} +{{ $root := dict "@context" "https://schema.org" "@graph" $graph }} +<script type="application/ld+json">{{ $root | jsonify | safeHTML }}</script> diff --git a/layouts/partials/clusters/sidebar_nav.html b/layouts/partials/clusters/sidebar_nav.html new file mode 100644 index 00000000000..f8e20c824a2 --- /dev/null +++ b/layouts/partials/clusters/sidebar_nav.html @@ -0,0 +1,39 @@ +{{/* Sidebar: link_mode "anchor" (#cluster-N on hub) or "subpath" (/clusters/cluster-N/ on subpages). active_cluster_number highlights + expands that group on subpages. */}} +{{ $data := .data }} +{{ $arrowColors := .arrowColors }} +{{ $link_mode := .link_mode | default "anchor" }} +{{ $activeN := int (.active_cluster_number | default -1) }} + +<div class="col-lg-4 col-xl-3 clusters-sidebar" id="clusters-sidebar"> + <div class="clusters-sidebar-inner"> + <div class="sidebar-header">{{ if eq $link_mode "subpath" }}Clusters{{ else }}Clusters & Sub-clusters{{ end }}</div> + <nav id="cluster-nav"> + {{ range $ci, $cluster := $data.clusters }} + {{ $cid := printf "cluster-%d" (int $cluster.number) }} + {{ $cn := int $cluster.number }} + {{ $isActive := eq $cn $activeN }} + {{ $clusterHref := cond (eq $link_mode "subpath") (printf "/clusters/cluster-%d/" (int $cluster.number) | relURL) (printf "#%s" $cid) }} + <div class="cluster-nav-group{{ if $isActive }} cluster-nav-group--active{{ end }}" data-cluster="{{ $cid }}"> + <a href="{{ $clusterHref }}" class="cluster-nav-heading{{ if $isActive }} cluster-nav-heading--active{{ end }}"{{ if $isActive }} aria-current="page"{{ end }}> + {{ $arrowColor := index $arrowColors (mod $ci (len $arrowColors)) }} + <span class="cluster-nav-toggle" style="color:{{ $arrowColor }};">▸</span> + {{ $cluster.name }} + </a> + <ul class="cluster-nav-subs" style="display:none;"> + {{ range $si, $sc := $cluster.sub_clusters }} + {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} + {{/* Subpath: include pane hash so the target tab opens after navigation */}} + {{ $subHref := cond (eq $link_mode "subpath") (printf "/clusters/cluster-%d/#%s" (int $cluster.number) $scid | relURL) (printf "#%s" $cid) }} + <li class="nav-item"> + <a href="{{ $subHref }}" class="nav-link sc-nav-link" data-cluster="{{ $cid }}" data-tab="{{ $scid }}-tab"> + {{ $sc.name }} + <span class="badge badge-pill">{{ len $sc.publications }}</span> + </a> + </li> + {{ end }} + </ul> + </div> + {{ end }} + </nav> + </div> +</div> diff --git a/layouts/partials/custom_head.html b/layouts/partials/custom_head.html new file mode 100644 index 00000000000..2d9d9b761f8 --- /dev/null +++ b/layouts/partials/custom_head.html @@ -0,0 +1,4 @@ +{{/* Site override: extra head tags (see theme academic site_head.html) */}} +{{ with .Params.keywords }} + <meta name="keywords" content="{{ delimit . ", " }}"> +{{ end }} diff --git a/layouts/partials/site_head.html b/layouts/partials/site_head.html index 0f45cd7cdca..ca63382d778 100644 --- a/layouts/partials/site_head.html +++ b/layouts/partials/site_head.html @@ -206,6 +206,11 @@ {{ $og_image = $featured_image.Permalink }} {{ $og_image_width = $featured_image.Width }} {{ $og_image_height = $featured_image.Height }} + {{ else if and .Params.sharing_image_resource (.Resources.GetMatch .Params.sharing_image_resource) }} + {{ $share_res := .Resources.GetMatch .Params.sharing_image_resource }} + {{ $og_image = $share_res.Permalink }} + {{ $og_image_width = $share_res.Width }} + {{ $og_image_height = $share_res.Height }} {{ else if .Params.header.image }} {{ $og_image = printf "%s/%s" $media_dir .Params.header.image | absURL }} {{ else if site.Params.sharing_image }} @@ -246,6 +251,8 @@ {{- with $og_image_alt -}} <meta property="og:image:alt" content="{{ . }}"> {{- end -}} + <meta name="twitter:card" content="summary_large_image"> + <meta name="twitter:image" content="{{ $og_image }}"> {{- end -}} <meta property="og:locale" content="{{ site.LanguageCode | default "en-us" }}"> {{ if .IsPage }} diff --git a/scripts/generate_cluster_pages.py b/scripts/generate_cluster_pages.py new file mode 100644 index 00000000000..88e95059cef --- /dev/null +++ b/scripts/generate_cluster_pages.py @@ -0,0 +1,68 @@ +#!/usr/bin/env python3 +"""Generate content/clusters/cluster-N/index.md from data/clusters_v4.json (re-run after JSON changes).""" +from __future__ import annotations + +import json +from pathlib import Path + +ROOT = Path(__file__).resolve().parents[1] +DATA = ROOT / "data" / "clusters_v4.json" + + +def toml_escape(s: str) -> str: + return s.replace("\\", "\\\\").replace('"', '\\"') + + +def main() -> None: + data = json.loads(DATA.read_text(encoding="utf-8")) + for c in data["clusters"]: + n = int(c["number"]) + name = c["name"] + slug = f"cluster-{n}" + desc = (c.get("description") or "").strip() + plain = " ".join(desc.split())[:260] + summary = f"FORRT Cluster {n}: {name}. {plain}".strip() + if len(summary) > 300: + summary = summary[:297] + "…" + + title = f"Cluster {n}: {name} — FORRT Open Science Taxonomy" + heading = f"Cluster {n}: {name}" + + kws = [ + f"FORRT cluster {n}", + "open science", + "reproducible research", + name, + ] + kw_toml = ", ".join(json.dumps(k) for k in kws) + + md = f"""+++ +type = "clusters" +layout = "cluster" +cluster_number = {n} +title = "{toml_escape(title)}" +heading_title = "{toml_escape(heading)}" +summary = "{toml_escape(summary)}" +description = "{toml_escape(summary)}" +sharing_title = "{toml_escape(title)}" +sharing_description = "{toml_escape(summary)}" + +keywords = [ {kw_toml} ] + +date = 2024-01-01 +draft = false + +[sitemap] + changefreq = "monthly" + priority = 0.85 ++++ +""" + + out = ROOT / "content" / "clusters" / slug / "index.md" + out.parent.mkdir(parents=True, exist_ok=True) + out.write_text(md, encoding="utf-8") + print("Wrote", out.relative_to(ROOT)) + + +if __name__ == "__main__": + main() diff --git a/static/js/clusters-page.js b/static/js/clusters-page.js index ed8154a3743..c5dacd2a9df 100644 --- a/static/js/clusters-page.js +++ b/static/js/clusters-page.js @@ -198,17 +198,73 @@ var mobileToggle = document.getElementById('clusters-mobile-toggle'); var sidebar = document.getElementById('clusters-sidebar'); var backToTopBtn = document.getElementById('clusters-back-to-top'); - var controls = root.querySelector('.clusters-controls'); + /* Toolbar may live under the page title (outside .clusters-layout) */ + var controls = document.querySelector('.clusters-controls'); var navbarEl = document.getElementById('navbar-main'); var mobileNavMq = window.matchMedia ? window.matchMedia('(max-width: 991.98px)') : null; + var clusterSubpage = document.querySelector('.clusters-cluster-subpage'); + var mainScrollEl = document.querySelector('.clusters-cluster-subpage__main-scroll'); function clustersNavIsMobileWidth() { return mobileNavMq && mobileNavMq.matches; } - /** Keep drawer below sticky controls; release body scroll when closed or desktop. */ + /** /clusters/cluster-N/: desktop main column is the scroll container */ + function useClusterSubpageMainScroll() { + if (!clusterSubpage || !mainScrollEl) return false; + if (clustersNavIsMobileWidth()) return false; + var oy = window.getComputedStyle(mainScrollEl).overflowY; + return oy === 'auto' || oy === 'scroll'; + } + + function updateClusterSubpageDrawerTop() { + if (!clusterSubpage || !clustersNavIsMobileWidth()) { + document.documentElement.style.removeProperty('--cluster-subpage-drawer-top'); + return; + } + var bar = clusterSubpage.querySelector('.clusters-cluster-subpage__head-wrap'); + if (bar) { + document.documentElement.style.setProperty( + '--cluster-subpage-drawer-top', + Math.ceil(bar.getBoundingClientRect().bottom) + 4 + 'px' + ); + } + } + + function updateClusterSubpageLayout() { + if (!clusterSubpage) { + document.documentElement.style.removeProperty('--cluster-subpage-sticky-top'); + document.documentElement.style.removeProperty('--cluster-subpage-drawer-top'); + return; + } + var navOff = getNavbarStickyOffsetPx(); + clusterSubpage.style.setProperty('--cluster-subpage-nav-offset', navOff + 'px'); + document.documentElement.style.setProperty( + '--cluster-subpage-sticky-top', + 'calc(' + navOff + 'px + env(safe-area-inset-top, 0px))' + ); + if (clustersNavIsMobileWidth()) { + clusterSubpage.style.removeProperty('--cluster-subpage-head-reserved'); + updateClusterSubpageDrawerTop(); + return; + } + document.documentElement.style.removeProperty('--cluster-subpage-drawer-top'); + var display = clusterSubpage.querySelector('.clusters-cluster-subpage__display'); + if (display) { + clusterSubpage.style.setProperty( + '--cluster-subpage-head-reserved', + Math.ceil(display.getBoundingClientRect().top) + 12 + 'px' + ); + } + } + + /** Hub: lock body when drawer open. Cluster subpage: dropdown below bar — keep page scroll. */ function syncClustersMobileBodyScrollLock() { if (!sidebar) return; + if (clusterSubpage && clustersNavIsMobileWidth()) { + document.body.style.overflow = ''; + return; + } if (!clustersNavIsMobileWidth() || !sidebar.classList.contains('sidebar-open')) { document.body.style.overflow = ''; } else { @@ -223,15 +279,19 @@ } function updateStickyLayoutMetrics() { - if (!controls) return; root.style.setProperty('--clusters-sticky-offset', getNavbarStickyOffsetPx() + 'px'); - root.style.setProperty('--clusters-controls-height', controls.offsetHeight + 'px'); + root.style.setProperty( + '--clusters-controls-height', + controls ? controls.offsetHeight + 'px' : '0px' + ); } function scheduleStickyLayoutMetrics() { updateStickyLayoutMetrics(); + updateClusterSubpageLayout(); requestAnimationFrame(function () { updateStickyLayoutMetrics(); + updateClusterSubpageLayout(); }); } @@ -255,14 +315,21 @@ if (window.ResizeObserver && navbarEl) { new ResizeObserver(scheduleStickyLayoutMetrics).observe(navbarEl); } + if (window.ResizeObserver && controls) { + new ResizeObserver(scheduleStickyLayoutMetrics).observe(controls); + } + if (window.ResizeObserver && clusterSubpage) { + new ResizeObserver(scheduleStickyLayoutMetrics).observe(clusterSubpage); + } /** * Scroll so el sits below the sticky stack (navbar + .clusters-controls search bar). - * Uses live layout after tab/panel updates (rAF). + * Cluster subpages: scroll the <main> column only (desktop). */ function scrollElementBelowStickyChrome(el) { if (!el) return; updateStickyLayoutMetrics(); + updateClusterSubpageLayout(); requestAnimationFrame(function () { requestAnimationFrame(function () { var margin = 14; @@ -273,6 +340,11 @@ var navbar = document.getElementById('navbar-main'); chromeBottom = navbar ? Math.ceil(navbar.getBoundingClientRect().bottom) : 72; } + if (useClusterSubpageMainScroll() && mainScrollEl) { + var delta = el.getBoundingClientRect().top - chromeBottom - margin; + mainScrollEl.scrollBy({ top: delta, behavior: 'smooth' }); + return; + } var elTopDoc = el.getBoundingClientRect().top + window.pageYOffset; var targetScroll = elTopDoc - chromeBottom - margin; window.scrollTo({ top: Math.max(0, targetScroll), behavior: 'smooth' }); @@ -280,6 +352,12 @@ }); } + /** True when sidebar link should use JS (same-page #anchor), not full navigation. */ + function isClustersInPageNavHref(anchorEl) { + var href = anchorEl && anchorEl.getAttribute('href'); + return !!(href && href.charAt(0) === '#'); + } + /** Tab anchor is .nav-link with href="#pane-id" pointing at .tab-pane inside clusters layout. */ function scrollToClusterTabPaneFromTrigger(tabAnchor) { if (!tabAnchor) return; @@ -298,12 +376,32 @@ sidebar.classList.toggle('sidebar-open'); this.classList.toggle('active'); scheduleStickyLayoutMetrics(); - syncClustersMobileBodyScrollLock(); + requestAnimationFrame(function () { + updateClusterSubpageDrawerTop(); + syncClustersMobileBodyScrollLock(); + }); }); } + if (clusterSubpage) { + window.addEventListener( + 'scroll', + function () { + if (clustersNavIsMobileWidth() && sidebar && sidebar.classList.contains('sidebar-open')) { + updateClusterSubpageDrawerTop(); + } + }, + { passive: true } + ); + } + root.querySelectorAll('.cluster-nav-heading').forEach(function (heading) { heading.addEventListener('click', function (e) { + /* /clusters/cluster-N/ links: navigate; #cluster-N on hub: expand + scroll in-page */ + if (!isClustersInPageNavHref(this)) { + closeClustersMobileSidebar(); + return; + } e.preventDefault(); var group = this.closest('.cluster-nav-group'); if (!group) return; @@ -318,12 +416,24 @@ if (clickedArrow) return; var clusterId = group.getAttribute('data-cluster'); var section = clusterId ? document.getElementById(clusterId) : null; - if (section) section.scrollIntoView({ behavior: 'smooth', block: 'start' }); + if (section) { + var scrollTarget = + section.querySelector('.cluster-header') || + section.querySelector('.cluster-title') || + section; + setTimeout(function () { + scrollElementBelowStickyChrome(scrollTarget); + }, 50); + } }); }); root.querySelectorAll('.sc-nav-link').forEach(function (link) { link.addEventListener('click', function (e) { + if (!isClustersInPageNavHref(this)) { + closeClustersMobileSidebar(); + return; + } e.preventDefault(); var clusterId = this.getAttribute('data-cluster'); var tabId = this.getAttribute('data-tab'); @@ -339,6 +449,20 @@ }); }); + /* e.g. /clusters/cluster-2/#c2-sc1 — open matching tab after load or hash-only navigation */ + function applyClusterUrlHashTab() { + var raw = window.location.hash.replace(/^#/, ''); + if (!raw || !/^c\d+-sc\d+$/.test(raw)) return; + var tab = document.getElementById(raw + '-tab'); + if (!tab) return; + showBootstrapTab(tab); + setTimeout(function () { + scrollToClusterTabPaneFromTrigger(tab); + }, 150); + } + applyClusterUrlHashTab(); + window.addEventListener('hashchange', applyClusterUrlHashTab); + /* Clicking sub-cluster tabs: scroll so pane content clears sticky chrome */ if (typeof window.jQuery !== 'undefined' && window.jQuery.fn.tab) { window @@ -496,12 +620,21 @@ if (backToTopBtn) { function toggleBackToTop() { - backToTopBtn.classList.toggle('is-visible', window.scrollY > 500); + var useMain = useClusterSubpageMainScroll(); + var show = useMain ? mainScrollEl.scrollTop > 400 : window.scrollY > 500; + backToTopBtn.classList.toggle('is-visible', show); } window.addEventListener('scroll', toggleBackToTop, { passive: true }); + if (mainScrollEl) { + mainScrollEl.addEventListener('scroll', toggleBackToTop, { passive: true }); + } toggleBackToTop(); backToTopBtn.addEventListener('click', function () { - window.scrollTo({ top: 0, behavior: 'smooth' }); + if (useClusterSubpageMainScroll() && mainScrollEl) { + mainScrollEl.scrollTo({ top: 0, behavior: 'smooth' }); + } else { + window.scrollTo({ top: 0, behavior: 'smooth' }); + } }); } }); From 3a68275dded2c9a1b9d4a69da0dbb587052dd757 Mon Sep 17 00:00:00 2001 From: Lukas Wallrich <lukas.wallrich@gmail.com> Date: Wed, 25 Mar 2026 16:34:20 +0000 Subject: [PATCH 08/11] Simplify clusters intro: concise text + lightbox image hero Replace verbose multi-paragraph intro with a compact two-column layout (text left, clickable thumbnail right) and remove syllabus section. Adds lightbox overlay with magnifying glass hint for discoverability. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --- assets/scss/custom.scss | 241 +++++++++------------------ layouts/partials/clusters/intro.html | 105 ++++-------- 2 files changed, 116 insertions(+), 230 deletions(-) diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index 794d7b5e3a9..1d60c5ec9ab 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -1445,212 +1445,129 @@ article.article:has(table) .article-container { margin-bottom: 0; } -/* Main introductory paragraphs */ -.intro-content { - line-height: 1.6; -} - -.intro-paragraph { - font-size: 0.95rem; - color: #444; - margin-bottom: 1.25rem; - line-height: 1.6; +/* Hero: text left, image right */ +.intro-hero { + display: flex; + align-items: center; + gap: 2rem; } -.intro-note { - font-size: 0.9rem; - color: #666; - background: rgba(255, 235, 205, 0.3); - padding: 0.75rem 1rem; - border-left: 3px solid #ff9800; - border-radius: 4px; - margin: 1.5rem 0; - font-style: italic; +.intro-hero-text { + flex: 1 1 60%; } -/* Numbered clusters list */ -.intro-clusters-list { - margin: 1.5rem 0 1.5rem 0; +.intro-hero-image { + flex: 0 0 auto; + max-width: 360px; } -.clusters-numbered-list { - font-size: 0.9rem; - color: #555; - padding-left: 1.5rem; +.intro-paragraph { + font-size: 0.95rem; + color: #444; + margin-bottom: 0; line-height: 1.7; } -.clusters-numbered-list li { - margin-bottom: 0.65rem; -} - -.clusters-numbered-list li::marker { - color: #6070a0; - font-weight: 600; -} - -/* Image section */ -.intro-image-wrapper { - margin: 1.25rem 0 0.5rem; - text-align: center; - padding: 0.85rem 0 0.6rem; - background: linear-gradient(135deg, rgba(202, 207, 220, 0.08) 0%, rgba(212, 228, 217, 0.08) 100%); - border-radius: 12px; -} - -.intro-figure { - margin: 0 auto; - display: block; - width: 100%; - max-width: 100%; -} - -.intro-image { +/* Thumbnail in the hero */ +.intro-thumbnail { width: 100%; - max-width: 100%; height: auto; - border-radius: 10px; - box-shadow: 0 8px 24px rgba(0, 0, 0, 0.12), 0 2px 6px rgba(0, 0, 0, 0.08); + border-radius: 8px; + box-shadow: 0 4px 14px rgba(0, 0, 0, 0.1); border: 2px solid rgba(255, 255, 255, 0.8); background: white; - padding: 4px; - display: block; + padding: 3px; + cursor: pointer; + transition: box-shadow 0.2s ease, transform 0.2s ease; } -.intro-figcaption { - font-size: 0.95rem; - color: #666; - margin-top: 0.55rem; - margin-bottom: 0; - font-weight: 500; - font-style: normal; +.intro-thumbnail:hover { + box-shadow: 0 6px 20px rgba(0, 0, 0, 0.18); + transform: scale(1.02); } -/* Use full container width on large screens (theme XL container = 1200px) */ -@media (min-width: 992px) { - .intro-image-wrapper { - padding: 1rem 0 0.75rem; - } - - .intro-image { - padding: 6px; - } -} - -@media (min-width: 1200px) { - .intro-image-wrapper { - margin: 1.35rem 0 0.55rem; - padding: 1.15rem 0 0.7rem; - } - - .intro-figcaption { - font-size: 1rem; - margin-top: 0.65rem; - } +.lightbox-trigger { + display: block; + text-decoration: none; + position: relative; } -/* Syllabus section */ -.intro-syllabus { - margin-top: 1rem; - margin-bottom: 0; - padding: 0.85rem 1.25rem 1.15rem; +/* "Click to enlarge" hint */ +.lightbox-hint { + display: flex; + align-items: center; + justify-content: center; + gap: 0.35rem; + margin-top: 0.5rem; + font-size: 0.78rem; + color: #6070a0; + opacity: 0.7; + transition: opacity 0.2s; } -.syllabus-heading { - font-size: 1.1rem; - font-weight: 700; - color: #333; - margin-bottom: 0.75rem; +.lightbox-trigger:hover .lightbox-hint { + opacity: 1; } -.syllabus-text { - font-size: 0.95rem; - color: #555; - margin-bottom: 1rem; - line-height: 1.5; +/* Lightbox overlay */ +.lightbox-overlay { + display: none; + position: fixed; + inset: 0; + z-index: 9999; + background: rgba(0, 0, 0, 0.8); + justify-content: center; + align-items: center; + cursor: pointer; } -.syllabus-links { +.lightbox-overlay.active { display: flex; - flex-wrap: wrap; - gap: 0.75rem; } -.syllabus-link { - display: inline-flex; - align-items: center; - gap: 0.5rem; - padding: 0.6rem 1rem; +.lightbox-image { + max-width: 90vw; + max-height: 90vh; + border-radius: 8px; + box-shadow: 0 8px 40px rgba(0, 0, 0, 0.4); background: white; - border: 1px solid #dee2e6; - border-radius: 6px; - color: #1c7ed6; - text-decoration: none; - font-size: 0.9rem; - font-weight: 500; - transition: all 0.2s ease; + padding: 6px; } -.syllabus-link:hover { - background: #ecf2ff; - border-color: #1c7ed6; - color: #0c5ba8; - text-decoration: none; - box-shadow: 0 2px 6px rgba(28, 126, 214, 0.1); +.lightbox-close { + position: absolute; + top: 1rem; + right: 1.5rem; + font-size: 2.5rem; + color: #fff; + background: none; + border: none; + cursor: pointer; + line-height: 1; + opacity: 0.8; + transition: opacity 0.2s; } -.link-icon { - font-size: 0.95rem; +.lightbox-close:hover { + opacity: 1; } -/* Responsive adjustments for clusters intro */ +/* Stack on small screens */ @media (max-width: 768px) { - .intro-paragraph { - font-size: 0.9rem; - } - - .clusters-numbered-list { - font-size: 0.85rem; - } - - .intro-syllabus { - margin-top: 0.85rem; - padding: 0.75rem 1rem 1rem; - } - - .syllabus-links { - gap: 0.5rem; - } - - .syllabus-link { - padding: 0.5rem 0.8rem; - font-size: 0.85rem; - } - - .intro-image-wrapper { - margin: 1.1rem 0 0.45rem; - padding: 0.65rem 0 0.5rem; + .intro-hero { + flex-direction: column; + gap: 1.25rem; } - .intro-image { - box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1); + .intro-hero-image { + max-width: 260px; } - .intro-figcaption { + .intro-paragraph { font-size: 0.9rem; } } -@media (max-width: 480px) { - .intro-image-wrapper { - margin: 1rem 0 0.35rem; - padding: 0.5rem 0 0.4rem; - } - - .intro-figure { - max-width: 100%; - } -} /* -------------------------------------------------- */ /* Clusters Page Section Styles */ diff --git a/layouts/partials/clusters/intro.html b/layouts/partials/clusters/intro.html index 0a4ac4d1740..a054324dbbf 100644 --- a/layouts/partials/clusters/intro.html +++ b/layouts/partials/clusters/intro.html @@ -1,78 +1,47 @@ -{{/* intro.html - Intro section for clusters page with matching styling */}} +{{/* intro.html - Concise intro with text left, lightbox image right */}} <div class="clusters-intro"> - - {{/* Main introductory text */}} - <div class="intro-content"> - <p class="intro-paragraph"> - In order to teach Open and Reproducible Science effectively, educators need to make sense of almost a decade of literature, across several fields, and be informed about ongoing (and often dynamic) debates. This is a tall ask for most educators. So FORRT sought to develop strategies and propose solutions to mitigate the effects of competing academic interests and help scholars implement open and reproducible science tenets in their teaching and mentoring workflow. - </p> - - <p class="intro-paragraph"> - In an effort to reduce some of the burden on educators wishing to learn or teach these concepts, FORRT has drawn on the expertise of more than 50 experts from its community to provide educators with a comprehensive but straightforward accessible didactic framework. FORRT clusters is a result of a comprehensive literature review guided by educational, pedagogical and didactic considerations aiming at providing a pathway towards the incremental adoption of Open and Reproducible Science tenets into educators/scholars teaching and mentoring. - </p> - - <p class="intro-paragraph"> - The focus lies not on simply aggregating the literature into bins, but on making sense of existing works, weaving connections where none exist, and providing a sensible learning-oriented Open and Reproducible Science taxonomy. FORRT taxonomy is composed of 11 clusters: - </p> + + <div class="intro-hero"> + {{/* Left column: text */}} + <div class="intro-hero-text"> + <p class="intro-paragraph"> + Teaching Open and Reproducible Science shouldn't require educators to spend months sifting through a decade of literature. FORRT simplifies this process by providing a curated, expert-backed framework. Developed by over 50 scholars, our taxonomy organizes open scholarship into 11 distinct clusters, offering a clear pathway for integrating these tenets into your teaching and mentoring, regardless of your field or level of expertise. + </p> + </div> + + {{/* Right column: lightbox image */}} + <div class="intro-hero-image"> + <a href="FORRT_Clusters.webp" class="lightbox-trigger" aria-label="View full-size FORRT Clusters diagram"> + <img src="FORRT_Clusters.webp" alt="FORRT's Clusters hierarchy diagram" class="intro-thumbnail" loading="lazy"> + <span class="lightbox-hint"> + <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><circle cx="11" cy="11" r="8"/><line x1="21" y1="21" x2="16.65" y2="16.65"/><line x1="11" y1="8" x2="11" y2="14"/><line x1="8" y1="11" x2="14" y2="11"/></svg> + Click to enlarge + </span> + </a> + </div> </div> - {{/* Clusters list */}} - <div class="intro-clusters-list"> - <ol class="clusters-numbered-list"> - <li>Replicability crisis and credibility revolution knowledge</li> - <li>Conceptual and statistical knowledge</li> - <li>Ways of working</li> - <li>Pre-analysis planning</li> - <li>Transparency and reproducibility in computation and analysis</li> - <li>FAIR data and materials</li> - <li>Publication sharing</li> - <li>Replication and meta-research</li> - <li>Academic structures and institutions</li> - <li>Qualitative Research</li> - <li>Research Integrity</li> - </ol> + {{/* Lightbox overlay */}} + <div class="lightbox-overlay" id="clusters-lightbox" role="dialog" aria-modal="true" aria-label="FORRT Clusters diagram"> + <button class="lightbox-close" aria-label="Close">×</button> + <img src="FORRT_Clusters.webp" alt="FORRT's Clusters hierarchy diagram" class="lightbox-image"> </div> - {{/* Clusters contain info note */}} - <div class="intro-content"> - <p class="intro-note"> - <strong>Note:</strong> These clusters contain information for quantitative and qualitative researchers. - </p> + <script> + (function() { + var trigger = document.querySelector('.lightbox-trigger'); + var overlay = document.getElementById('clusters-lightbox'); + var closeBtn = overlay.querySelector('.lightbox-close'); - <p class="intro-paragraph"> - We further break down each cluster into sub-categories to provide educators/scholars with useful information on the extent of open scholarship, and how they are connected to one another. The idea behind specifying clusters and sub-clusters is to highlight that we have drawn fuzzy boundaries between clusters, while allowing for diversification and heterogeneity in how each educator integrates these cluster/sub-clusters with their respective field content. The breakdown of each cluster into sub-categories provides scholars with useful information on the extent of open science scholarship, and how they are connected to one another. - </p> + function open(e) { e.preventDefault(); overlay.classList.add('active'); } + function close() { overlay.classList.remove('active'); } - <p class="intro-paragraph"> - See below for each cluster, its description, sub-clusters, and associated works geared for teaching. And here's an attempt to visualize FORRT's clusters: - </p> - </div> + trigger.addEventListener('click', open); + closeBtn.addEventListener('click', close); + overlay.addEventListener('click', function(e) { if (e.target === overlay) close(); }); + document.addEventListener('keydown', function(e) { if (e.key === 'Escape') close(); }); + })(); + </script> - {{/* Clusters visualization image */}} - <div class="intro-image-wrapper"> - <figure class="intro-figure"> - <img src="FORRT_Clusters.webp" alt="FORRT's Clusters hierarchy diagram" class="intro-image"> - <figcaption class="intro-figcaption">FORRT's Clusters Overview</figcaption> - </figure> - </div> - - {{/* Syllabus section */}} - <div class="intro-syllabus"> - <h2 class="syllabus-heading">FORRT's Syllabus</h2> - <p class="syllabus-text"> - Building on the clusters we created a <strong>"Open and Reproducible Science" Syllabus</strong>. We hope it can serve as a starting point for your class. - </p> - <div class="syllabus-links"> - <a href="FORRT_O&R_101_Syllabus.pdf" class="syllabus-link" target="_blank" rel="noopener"> - <span class="link-icon">📄</span> PDF Download - </a> - <a href="https://docs.google.com/document/d/1pfFro5MbwBHzzXTeM_lE1gjFuq7AnnKWSDWkVwOBAtE/edit#" class="syllabus-link" target="_blank" rel="noopener"> - <span class="link-icon">📝</span> Editable G-doc - </a> - <a href="/syllabus/" target="_blank" rel="noopener" class="syllabus-link"> - <span class="link-icon">📚</span> Syllabus Page - </a> - </div> - </div> </div> From 331b813a764bdf6297704b19ec0e822bb1beb929 Mon Sep 17 00:00:00 2001 From: Lukas Wallrich <lukas.wallrich@gmail.com> Date: Wed, 25 Mar 2026 16:40:02 +0000 Subject: [PATCH 09/11] Update clusters intro: 100+ scholars, remove stale date Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --- content/clusters/_index.md | 1 - layouts/partials/clusters/intro.html | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/content/clusters/_index.md b/content/clusters/_index.md index 19756247601..0a0fcdf99ab 100644 --- a/content/clusters/_index.md +++ b/content/clusters/_index.md @@ -23,7 +23,6 @@ sharing_image_alt = "Diagram of FORRT's eleven open science clusters taxonomy" keywords = [ "open science clusters", "reproducible research", "FORRT taxonomy", "replicability", "open scholarship", "research transparency", "FAIR data", "meta-research", "research integrity", "teaching open science" ] -date = 2024-01-01 draft = false [sitemap] diff --git a/layouts/partials/clusters/intro.html b/layouts/partials/clusters/intro.html index a054324dbbf..371b2e27d81 100644 --- a/layouts/partials/clusters/intro.html +++ b/layouts/partials/clusters/intro.html @@ -5,7 +5,7 @@ {{/* Left column: text */}} <div class="intro-hero-text"> <p class="intro-paragraph"> - Teaching Open and Reproducible Science shouldn't require educators to spend months sifting through a decade of literature. FORRT simplifies this process by providing a curated, expert-backed framework. Developed by over 50 scholars, our taxonomy organizes open scholarship into 11 distinct clusters, offering a clear pathway for integrating these tenets into your teaching and mentoring, regardless of your field or level of expertise. + Teaching Open and Reproducible Science shouldn't require educators to spend months sifting through a decade of literature. FORRT simplifies this process by providing a curated, expert-backed framework. Developed by over 100 scholars, our taxonomy organizes open scholarship into 11 distinct clusters, offering a clear pathway for integrating these tenets into your teaching and mentoring, regardless of your field or level of expertise. </p> </div> From 43d02f083c10efc2d67f1421404800fb42c529ca Mon Sep 17 00:00:00 2001 From: Lukas Wallrich <lukas.wallrich@gmail.com> Date: Wed, 25 Mar 2026 17:03:32 +0000 Subject: [PATCH 10/11] UI polish: 3-col sub-cluster grid, full-width layout, update badge - Sub-cluster tabs in fixed 3-column grid with fixed height and centered text - Remove reference counts from tabs - Full-width layout for clusters display section - Darker background on inactive tabs - "Update pending" badge on clusters diagram Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --- assets/scss/custom.scss | 88 ++++++++++++------- layouts/clusters/single.html | 5 +- .../partials/clusters/cluster_section.html | 3 +- layouts/partials/clusters/intro.html | 5 +- 4 files changed, 62 insertions(+), 39 deletions(-) diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index 1d60c5ec9ab..0ffcfea1724 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -418,41 +418,42 @@ max-width: 48rem; } -/* ---- Sub-cluster tabs (chip style + border: same on desktop & mobile) ---- */ +/* ---- Sub-cluster tabs (3-column grid, text clamped to 3 lines) ---- */ .cluster-tabs { - flex-wrap: wrap; - gap: 0.35rem 0.3rem; + display: grid; + grid-template-columns: repeat(3, 1fr); + gap: 0.35rem; margin-bottom: 0; - overflow: visible; - align-items: stretch; border-bottom: none; } .cluster-tabs .nav-item { - flex: 0 1 auto; min-width: 0; - max-width: 100%; } .cluster-tabs .nav-link { font-size: 0.78rem; padding: 0.4rem 0.75rem; color: #8b0000; - white-space: normal; - word-break: break-word; - hyphens: auto; text-align: center; line-height: 1.25; - min-height: 2.35rem; - display: flex; - align-items: center; - justify-content: center; - flex-wrap: wrap; - gap: 0.15rem; + height: 3.35rem; margin-bottom: 0; border-radius: 6px; border: 1px solid rgba(0, 0, 0, 0.1); + background: rgba(0, 0, 0, 0.2); transition: background 0.15s, color 0.15s, border-color 0.15s; + display: flex; + align-items: center; + justify-content: center; + overflow: hidden; +} + +.tab-label { + display: -webkit-box; + -webkit-line-clamp: 3; + -webkit-box-orient: vertical; + overflow: hidden; } .cluster-tabs .nav-link:hover { @@ -468,13 +469,6 @@ border-color: rgba(0, 0, 0, 0.2); } -.tab-count { - font-size: 0.6rem; - color: #aaa; - margin-left: 0.15em; - font-weight: 400; -} - .cluster-tab-content { padding: 1.25rem 0.5rem; border-top: 1px solid rgba(0, 0, 0, 0.1); @@ -609,10 +603,8 @@ margin: 0; } - /* Narrow screens: sized tab cells (base styles = borders match desktop) */ - .cluster-tabs .nav-item { - flex: 1 1 auto; - min-width: clamp(7rem, 42vw, 11.5rem); + .cluster-tabs { + grid-template-columns: repeat(2, 1fr); } .cluster-tab-content { @@ -735,7 +727,7 @@ } .cluster-tabs .nav-link { - min-height: 2rem; + height: 2.8rem; padding: 0.34rem 0.44rem; } @@ -749,14 +741,9 @@ margin-top: 0.45rem; } - .cluster-tabs .nav-item { - min-width: calc(50% - 0.2rem); - flex: 1 1 calc(50% - 0.2rem); - } - .cluster-tabs .nav-link { font-size: 0.66rem; - min-height: 1.9rem; + height: 2.5rem; border-radius: 5px; } @@ -1486,6 +1473,26 @@ article.article:has(table) .article-container { transform: scale(1.02); } +.intro-thumbnail-wrapper { + position: relative; + display: inline-block; +} + +.update-pending-badge { + position: absolute; + bottom: 0.5rem; + left: 50%; + transform: translateX(-50%); + background: rgba(0, 0, 0, 0.65); + color: #fff; + font-size: 0.7rem; + font-weight: 600; + padding: 0.2rem 0.6rem; + border-radius: 4px; + letter-spacing: 0.03em; + white-space: nowrap; +} + .lightbox-trigger { display: block; text-decoration: none; @@ -1573,6 +1580,19 @@ article.article:has(table) .article-container { /* Clusters Page Section Styles */ /* -------------------------------------------------- */ +/* Full-width cluster layout */ +.cluster-full-width { + max-width: 100% !important; + padding: 15px !important; + margin: 15px !important; +} + +.cluster-full-width .container { + max-width: 100% !important; + padding: 15px !important; + margin: 15px !important; +} + .clusters-intro-section { background: linear-gradient(to bottom, #fefdf6 0%, #f9f8f5 100%); padding: 0.5rem 0 0.5rem; diff --git a/layouts/clusters/single.html b/layouts/clusters/single.html index 7c2e3be0953..d9752f639d1 100644 --- a/layouts/clusters/single.html +++ b/layouts/clusters/single.html @@ -1,5 +1,6 @@ {{/* layouts/clusters/single.html - Main layout for clusters page (same H1/SEO split as list.html) */}} {{ define "main" }} + {{ partial "clusters/seo_jsonld.html" . }} <div class="universal-wrapper pt-3 pb-3"> <div class="container"> @@ -14,7 +15,7 @@ <div class="article-container pt-3"> {{/* Hub /clusters/ only: larger H1 (cluster subpages use layout cluster, not this template) */}} <h1 class="clusters-site-heading{{ if and .IsNode (eq .Section "clusters") }} clusters-hub-page__title{{ end }}" itemprop="headline">{{ .Params.heading_title | default .Title }}</h1> - + {{/* Subtitle if present */}} {{ if .Params.subtitle }} <p class="page-subtitle">{{ .Params.subtitle | markdownify }}</p> @@ -47,7 +48,7 @@ <h1 class="clusters-site-heading{{ if and .IsNode (eq .Section "clusters") }} cl </section> {{/* CLUSTERS DISPLAY SECTION - The main clusters content */}} - <section class="clusters-display-section"> + <section class="cluster-full-width clusters-display-section"> <div class="container"> {{ partial "clusters/all_clusters.html" . }} </div> diff --git a/layouts/partials/clusters/cluster_section.html b/layouts/partials/clusters/cluster_section.html index b62aecfb463..91490cc0fac 100644 --- a/layouts/partials/clusters/cluster_section.html +++ b/layouts/partials/clusters/cluster_section.html @@ -27,8 +27,7 @@ <h2 class="cluster-title"> <a class="nav-link{{ if eq $si 0 }} active{{ end }}" id="{{ $scid }}-tab" data-toggle="tab" href="#{{ $scid }}" role="tab" aria-controls="{{ $scid }}" aria-selected="{{ if eq $si 0 }}true{{ else }}false{{ end }}"> - {{ $sc.name }} - <span class="tab-count">{{ len $sc.publications }}</span> + <span class="tab-label">{{ $sc.name }}</span> </a> </li> {{ end }} diff --git a/layouts/partials/clusters/intro.html b/layouts/partials/clusters/intro.html index 371b2e27d81..41ebf144439 100644 --- a/layouts/partials/clusters/intro.html +++ b/layouts/partials/clusters/intro.html @@ -12,7 +12,10 @@ {{/* Right column: lightbox image */}} <div class="intro-hero-image"> <a href="FORRT_Clusters.webp" class="lightbox-trigger" aria-label="View full-size FORRT Clusters diagram"> - <img src="FORRT_Clusters.webp" alt="FORRT's Clusters hierarchy diagram" class="intro-thumbnail" loading="lazy"> + <div class="intro-thumbnail-wrapper"> + <img src="FORRT_Clusters.webp" alt="FORRT's Clusters hierarchy diagram" class="intro-thumbnail" loading="lazy"> + <span class="update-pending-badge">Update pending</span> + </div> <span class="lightbox-hint"> <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><circle cx="11" cy="11" r="8"/><line x1="21" y1="21" x2="16.65" y2="16.65"/><line x1="11" y1="8" x2="11" y2="14"/><line x1="8" y1="11" x2="14" y2="11"/></svg> Click to enlarge From 08193a597341456f2a1ff64179f369d698e4ef99 Mon Sep 17 00:00:00 2001 From: Lukas Wallrich <lukas.wallrich@gmail.com> Date: Wed, 25 Mar 2026 22:06:45 +0000 Subject: [PATCH 11/11] Clean up clusters code: remove dead CSS/JS, fix redundancies, align nav behavior - Remove ~145 lines of dead .clusters-cluster-subpage CSS and ~65 lines of dead JS (element never exists in DOM) - Remove unused list.html template and .clusters-title-toolbar CSS - Extract duplicated color arrays to shared partial (colors.html) - Remove duplicate intro text from _index.md (was inconsistent with intro.html) - Fix sub-cluster nav on individual pages to use in-page anchors for the active cluster, aligning scroll behavior with the hub page - Fix redundant .toLowerCase() in search - Add min-height on .cluster-tab-content to keep footer below fold when viewing short sub-clusters Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --- assets/scss/custom.scss | 228 ++++-------------- content/clusters/_index.md | 2 - content/clusters/cluster-2/index.md | 2 +- content/clusters/cluster-3/index.md | 6 +- data/clusters_v4.json | 20 +- layouts/clusters/cluster.html | 31 +-- layouts/clusters/list.html | 45 ---- layouts/partials/clusters/all_clusters.html | 5 +- .../partials/clusters/clusters_controls.html | 4 + layouts/partials/clusters/colors.html | 4 + layouts/partials/clusters/sidebar_nav.html | 18 +- static/js/clusters-page.js | 208 +++++++--------- 12 files changed, 194 insertions(+), 379 deletions(-) delete mode 100644 layouts/clusters/list.html create mode 100644 layouts/partials/clusters/colors.html diff --git a/assets/scss/custom.scss b/assets/scss/custom.scss index 0ffcfea1724..bae960b345b 100644 --- a/assets/scss/custom.scss +++ b/assets/scss/custom.scss @@ -140,10 +140,6 @@ padding-top: 0; } -.clusters-sidebar-inner #cluster-nav > .cluster-nav-group:first-child.cluster-nav-group--active { - padding-top: 0; - margin-top: 0; -} .cluster-nav-heading { display: flex; @@ -164,29 +160,7 @@ color: #111; } -/* Current cluster on /clusters/cluster-N/ (see active_cluster_number in sidebar_nav) */ -.cluster-nav-group--active { - margin: 0 -0.15rem 0.35rem; - padding: 0.25rem 0.2rem 0.3rem; - border-radius: 6px; - background: rgba(139, 0, 0, 0.07); - border: 1px solid rgba(139, 0, 0, 0.14); -} - -.cluster-nav-heading--active { - color: #5a0000 !important; - background: rgba(255, 255, 255, 0.72); - font-weight: 700; -} - -.cluster-nav-heading--active:hover { - background: rgba(255, 255, 255, 0.88); - color: #3d0000 !important; -} - -.cluster-nav-group--active .cluster-nav-subs .nav-link { - color: #444; -} +/* Active cluster on subpages — no special styling, looks same as hub */ .cluster-nav-toggle { display: inline-block; @@ -274,11 +248,6 @@ margin-bottom: 0.75rem; } -/* Search bar sits under page title (universal-wrapper); spacing via .mb-3 on wrapper */ -.clusters-title-toolbar { - max-width: 100%; -} - /* ---- Inline clusters list search (toolbar; not Algolia/site search) ---- */ .clusters-inline-search { position: relative; @@ -314,6 +283,31 @@ border-radius: 6px; } +.clusters-inline-search__option-label { + display: inline-flex; + align-items: center; + gap: 0.35rem; + font-size: 0.78rem; + color: #666; + cursor: pointer; + user-select: none; + margin: 0 0 0 0.5rem; + white-space: nowrap; +} + +.clusters-inline-search__option-label input[type="checkbox"] { + margin: 0; + cursor: pointer; +} + +.clusters-inline-search__hit-icon { + flex-shrink: 0; + color: #999; + font-size: 0.7rem; + align-self: flex-start; + margin-top: 0.2rem; +} + .clusters-inline-search__toolbar { display: flex; align-items: center; @@ -380,9 +374,9 @@ .clusters-inline-search__hit { display: flex; - flex-direction: column; + flex-direction: row; align-items: flex-start; - gap: 0.2rem; + gap: 0.4rem; padding: 0.5rem 0.75rem; border-bottom: 1px solid #f0f0f0; color: #333; @@ -391,10 +385,21 @@ text-align: left; } +.clusters-inline-search__hit-text { + display: flex; + flex-direction: column; + gap: 0.15rem; + min-width: 0; +} + .clusters-inline-search__hit-label { line-height: 1.35; } +.clusters-inline-search__hit--publication .clusters-inline-search__hit-label { + font-size: 0.72rem; +} + .clusters-inline-search__hit-meta { font-size: 0.68rem; color: #888; @@ -535,8 +540,7 @@ @media (max-width: 991px) { /* Flush under sticky controls (no mb-3 gap) + drawer meets toggle bar */ - .clusters-layout .clusters-controls, - .clusters-title-toolbar .clusters-controls { + .clusters-layout .clusters-controls { margin-bottom: 0 !important; } @@ -1584,13 +1588,19 @@ article.article:has(table) .article-container { .cluster-full-width { max-width: 100% !important; padding: 15px !important; - margin: 15px !important; + margin-left: 15px !important; + margin-right: 15px !important; + margin-top: 0 !important; + margin-bottom: 0 !important; } .cluster-full-width .container { max-width: 100% !important; padding: 15px !important; - margin: 15px !important; + margin-left: 15px !important; + margin-right: 15px !important; + margin-top: 0 !important; + margin-bottom: 0 !important; } .clusters-intro-section { @@ -1607,148 +1617,6 @@ article.article:has(table) .article-container { border-bottom: 1px solid #e9ecef; } -/* ---- /clusters/cluster-N/ only: sticky title + search; <main> scrolls (desktop) ---- */ -/* Sticky on __head-wrap (not inner) — more reliable on iOS/mobile. */ -/* --cluster-subpage-sticky-top on :root (JS). z-index < navbar 1030. */ -.clusters-cluster-subpage { - overflow: visible; -} - -/* Opaque band so scrolled content doesn’t show through; full viewport width (overrides .universal-wrapper 1000px cap). */ -.clusters-cluster-subpage__head-wrap.universal-wrapper { - position: -webkit-sticky; - position: sticky; - top: var(--cluster-subpage-sticky-top, 72px); - z-index: 1018; - overflow: visible; - width: 100%; - max-width: none; - /* Match site base background (foundation) so it blends into the page. */ - background: #fefdf6; - box-shadow: none; -} - -.clusters-cluster-subpage__head-inner { - /* Match site base background (foundation) so it blends into the page. */ - background: #fefdf6; - padding-bottom: 0; - display: flex; - flex-direction: column; - align-items: center; - text-align: center; -} - -/* Center breadcrumb title row + wrapped lines */ -.clusters-cluster-subpage__head-inner .clusters-heading-row__crumbs { - justify-content: center; -} - -.clusters-cluster-subpage__head-inner .clusters-heading-row__title.clusters-site-heading { - flex: 0 1 auto; - text-align: center; -} - -.clusters-cluster-subpage__head-inner .clusters-title-toolbar { - width: 100%; - max-width: 32rem; - display: flex; - flex-direction: column; - align-items: stretch; -} - -.clusters-cluster-subpage__head-inner .clusters-inline-search__row { - justify-content: center; -} - -.clusters-cluster-subpage__head-inner .clusters-mobile-toggle { - text-align: center; -} - -/* No “card” behind search on cluster subpages */ -.clusters-cluster-subpage .clusters-controls { - position: static; - top: auto; - z-index: auto; - width: 100%; - max-width: 32rem; - margin-left: auto; - margin-right: auto; - margin-bottom: 0.25rem !important; - padding: 0.35rem 0; - background: transparent !important; - border: none !important; - box-shadow: none !important; -} - -.clusters-cluster-subpage__display.clusters-display-section { - /* Same foundation bg as .clusters-cluster-subpage__head-wrap */ - background: #fefdf6; - padding-top: 0.25rem; - margin-top: 0; - border-top: none; -} - -@media (min-width: 992px) { - .clusters-cluster-subpage__display { - overflow: hidden; - padding-top: 0.15rem; - } - - .clusters-layout--cluster-subpage .clusters-cluster-subpage__row { - align-items: stretch; - max-height: calc(100vh - var(--cluster-subpage-head-reserved, 220px)); - min-height: 280px; - } - - .clusters-cluster-subpage__main-scroll { - overflow-x: hidden; - overflow-y: auto; - -webkit-overflow-scrolling: touch; - overscroll-behavior: contain; - max-height: calc(100vh - var(--cluster-subpage-head-reserved, 220px)); - min-height: 0; - padding-bottom: 2rem; - } - - .clusters-cluster-subpage .clusters-sidebar { - display: flex; - flex-direction: column; - min-height: 0; - max-height: calc(100vh - var(--cluster-subpage-head-reserved, 220px)); - overflow: hidden; - } - - .clusters-cluster-subpage .clusters-sidebar-inner { - position: static !important; - top: auto !important; - flex: 1 1 auto; - min-height: 0; - max-height: none; - overflow-y: auto; - -webkit-overflow-scrolling: touch; - } -} - -@media (max-width: 991.98px) { - .clusters-cluster-subpage__main-scroll { - max-height: none !important; - overflow-y: visible !important; - } - - /* Drawer drops below title/search bar instead of full-height sheet from old top */ - .clusters-cluster-subpage .clusters-sidebar.sidebar-open { - top: var(--cluster-subpage-drawer-top, 200px); - bottom: auto; - /* Sass min() shadows CSS min(); pass through as unquoted string for the compiler */ - max-height: #{"min(78vh, calc(100dvh - var(--cluster-subpage-drawer-top, 200px) - env(safe-area-inset-bottom, 0px) - 8px))"}; - border-radius: 0 0 10px 10px; - box-shadow: 0 10px 28px rgba(0, 0, 0, 0.18); - border-top: 1px solid #dee2e6; - z-index: 1024; - padding-bottom: 0.75rem; - } -} - /* Hub + /clusters/cluster-N/ — smaller than default Academic article H1 */ h1.clusters-site-heading { font-size: 1.45rem; diff --git a/content/clusters/_index.md b/content/clusters/_index.md index 0a0fcdf99ab..1f3c1fb32fb 100644 --- a/content/clusters/_index.md +++ b/content/clusters/_index.md @@ -29,5 +29,3 @@ draft = false changefreq = "monthly" priority = 0.9 +++ - -Teaching Open and Reproducible Science shouldn't require educators to spend months sifting through a decade of literature. FORRT simplifies this process by providing a curated, expert-backed framework. Developed by over 50 scholars, our taxonomy organizes open scholarship into 11 distinct clusters, offering a clear pathway for integrating these tenets into your teaching and mentoring, regardless of your field or level of expertise. diff --git a/content/clusters/cluster-2/index.md b/content/clusters/cluster-2/index.md index d826f9fbe46..f2e094aeb4b 100644 --- a/content/clusters/cluster-2/index.md +++ b/content/clusters/cluster-2/index.md @@ -3,7 +3,7 @@ type = "clusters" layout = "cluster" cluster_number = 2 title = "Cluster 2: Conceptual and Statistical Knowledge — FORRT Open Science Taxonomy" -heading_title = "Conceptual and Statistical Knowledge" +heading_title = "Cluster 2: Conceptual and Statistical Knowledge" summary = "FORRT Cluster 2: Conceptual and Statistical Knowledge. Attainment of a grounding in fundamental statistics, measurement, and its implications encompassing conceptual knowledge, application, interpretation and communication of statistical analyses. There are 8 sub-clusters which aim to further par…" description = "FORRT Cluster 2: Conceptual and Statistical Knowledge. Attainment of a grounding in fundamental statistics, measurement, and its implications encompassing conceptual knowledge, application, interpretation and communication of statistical analyses. There are 8 sub-clusters which aim to further par…" sharing_title = "Cluster 2: Conceptual and Statistical Knowledge — FORRT Open Science Taxonomy" diff --git a/content/clusters/cluster-3/index.md b/content/clusters/cluster-3/index.md index 8074875287a..cdc2c83d76c 100644 --- a/content/clusters/cluster-3/index.md +++ b/content/clusters/cluster-3/index.md @@ -4,10 +4,10 @@ layout = "cluster" cluster_number = 3 title = "Cluster 3: Ways of Working — FORRT Open Science Taxonomy" heading_title = "Cluster 3: Ways of Working" -summary = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:" -description = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:" +summary = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[s]:" +description = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[s]:" sharing_title = "Cluster 3: Ways of Working — FORRT Open Science Taxonomy" -sharing_description = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:" +sharing_description = "FORRT Cluster 3: Ways of Working. Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[s]:" keywords = [ "FORRT cluster 3", "open science", "reproducible research", "Ways of Working" ] diff --git a/data/clusters_v4.json b/data/clusters_v4.json index 000c85d377b..08438246203 100644 --- a/data/clusters_v4.json +++ b/data/clusters_v4.json @@ -189,6 +189,11 @@ "doi": "10.1177/1745691612460687", "apa": "Stroebe, W., Postmes, T., & Spears, R. (2012). Scientific Misconduct and the Myth of Self-Correction in Science. Perspectives on Psychological Science, 7(6), 670–688. https://doi.org/10.1177/1745691612460687", "auto_ref": true + }, + { + "doi": "10.1177/1556264614552421", + "apa": "Tijdink, J. K., Verbeke, R., & Smulders, Y. M. (2014). Publication Pressure and Scientific Misconduct in Medical Scientists. Journal of Empirical Research on Human Research Ethics, 9(5), 64–71. https://doi.org/10.1177/1556264614552421", + "auto_ref": true } ] }, @@ -478,6 +483,11 @@ "apa": "Kathawalla, U.-K., Silverstein, P., & Syed, M. (2021). Easing Into Open Science: A Guide for Graduate Students and Their Advisors. Collabra: Psychology, 7(1). https://doi.org/10.1525/collabra.18684", "auto_ref": true }, + { + "doi": "10.1098/rsos.251997", + "apa": "Krähmer, D., Schächtele, L., & Auspurg, K. (2026). Code sharing and reproducibility in survey-based social research: evidence from a large-scale audit. Royal Society Open Science, 13(3). https://doi.org/10.1098/rsos.251997", + "auto_ref": true + }, { "doi": "10.1177/2515245918810225", "apa": "Klein, R. A., Vianello, M., Hasselman, F., Adams, B. G., Adams, R. B., Alper, S., Aveyard, M., Axt, J. R., Babalola, M. T., Bahník, Š., Batra, R., Berkics, M., Bernstein, M. J., Berry, D. R., Bialobrzeska, O., Binan, E. D., Bocian, K., Brandt, M. J., Busching, R., … Nosek, B. A. (2018). Many Labs 2: Investigating Variation in Replicability Across Samples and Settings. Advances in Methods and Practices in Psychological Science, 1(4), 443–490. https://doi.org/10.1177/2515245918810225", @@ -1231,7 +1241,7 @@ { "number": 3, "name": "Ways of Working", - "description": "Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[r]:", + "description": "Attainment of an understanding of how research is conducted, managed and disseminated. There are 12 sub-clusters which aim to further parse the learning and teaching process[s]:", "sub_clusters": [ { "name": "Qualitative research", @@ -3292,7 +3302,7 @@ { "number": 8, "name": "Replication and meta-research", - "description": "Attainment of a grounding in 'replication research', which takes a variety of forms, each with a different purpose and contribution. Replicable science requires replication research. When teaching, students should understand the purpose and need of replications in its variety of forms and be able to conduct (and join) replication projects. There are 6 sub-clusters which aim to further parse the learning and teaching process:[af][ag]", + "description": "Attainment of a grounding in 'replication research', which takes a variety of forms, each with a different purpose and contribution. Replicable science requires replication research. When teaching, students should understand the purpose and need of replications in its variety of forms and be able to conduct (and join) replication projects. There are 6 sub-clusters which aim to further parse the learning and teaching process:[ag][ah]", "sub_clusters": [ { "name": "Conducting replication studies; challenges, limitations, and comparisons with the original study", @@ -3727,7 +3737,7 @@ }, { "name": "The politics of replicating famous studies", - "description": "Sometimes responses to replication research can be negative. Failed replications of famous work, most notably power posing, ego depletion, stereotype threat, and facial feedback[ah][ai], have received a lot of attention.", + "description": "Sometimes responses to replication research can be negative. Failed replications of famous work, most notably power posing, ego depletion, stereotype threat, and facial feedback[ai][aj], have received a lot of attention.", "publications": [ { "doi": "10.1371/journal.pone.0029081", @@ -4970,7 +4980,7 @@ }, { "name": "Sexuality & Gender", - "description": "Sexuality refers to the various aspects of an individual’s being related to their sexual feelings, thoughts, attractions and behaviour. We use “LGBTQ+” as an inclusive term to refer to all sexual identities and orientations which are not heterosexual. This includes but is not limited to lesbian, gay, bisexual, pansexual, asexual, queer, and questioning[ao].", + "description": "Sexuality refers to the various aspects of an individual’s being related to their sexual feelings, thoughts, attractions and behaviour. We use “LGBTQ+” as an inclusive term to refer to all sexual identities and orientations which are not heterosexual. This includes but is not limited to lesbian, gay, bisexual, pansexual, asexual, queer, and questioning[ap].", "publications": [ { "doi": "10.1126/sciadv.abe0933", @@ -6434,7 +6444,7 @@ { "number": 11, "name": "Research Integrity", - "description": "Research Integrity (RI) encompasses the moral and professional standards that ensure research is trustworthy, transparent, and ethical from inception to publication​. Traditionally, RI efforts have centered on preventing misconduct—the blatant fabrication, falsification, or plagiarism (FFP) that betrays the core of science. Modern perspectives, however, advocate a holistic vision: cultivating a culture of responsible, equitable, and open research practices that goes beyond avoiding misconduct to actively promoting excellence and fairness. Supervision, mentorship, and everyday collegial relations have an important part in cultivating a culture of research integrity and shaping what “good practice” looks like in labs and teams to new researchers. This includes how power dynamics, authorship, and credit are negotiated. Institutions matter too, policies, incentives, workload, and leadership either enable or erode integrity. RI is intrinsically linked with the Open Science movement. Both strive to make research more transparent and accountable, thereby strengthening credibility and public trust​. Open Science initiatives (e.g. data sharing, preregistration, open access) can make misconduct easier to detect and discourage, while fostering norms of honesty and rigor. Conversely, RI provides the ethical foundation for openness – emphasizing values like honesty, accountability, respect, and fairness that guide how openness is pursued. By making research integrity “possible, easy, normative, and rewarding” (Haven et al., 2022)​, institutions and communities create an environment where ethical, inclusive, and rigorous research thrives. Ultimately, RI is about more than rule-following; it is about embedding integrity as a fundamental ethos of research design, conduct, and dissemination – ensuring science advances knowledge and the public good in tandem.[as]", + "description": "Research Integrity (RI) encompasses the moral and professional standards that ensure research is trustworthy, transparent, and ethical from inception to publication​. Traditionally, RI efforts have centered on preventing misconduct—the blatant fabrication, falsification, or plagiarism (FFP) that betrays the core of science. Modern perspectives, however, advocate a holistic vision: cultivating a culture of responsible, equitable, and open research practices that goes beyond avoiding misconduct to actively promoting excellence and fairness. Supervision, mentorship, and everyday collegial relations have an important part in cultivating a culture of research integrity and shaping what “good practice” looks like in labs and teams to new researchers. This includes how power dynamics, authorship, and credit are negotiated. Institutions matter too, policies, incentives, workload, and leadership either enable or erode integrity. RI is intrinsically linked with the Open Science movement. Both strive to make research more transparent and accountable, thereby strengthening credibility and public trust​. Open Science initiatives (e.g. data sharing, preregistration, open access) can make misconduct easier to detect and discourage, while fostering norms of honesty and rigor. Conversely, RI provides the ethical foundation for openness – emphasizing values like honesty, accountability, respect, and fairness that guide how openness is pursued. By making research integrity “possible, easy, normative, and rewarding” (Haven et al., 2022)​, institutions and communities create an environment where ethical, inclusive, and rigorous research thrives. Ultimately, RI is about more than rule-following; it is about embedding integrity as a fundamental ethos of research design, conduct, and dissemination – ensuring science advances knowledge and the public good in tandem.[at]", "sub_clusters": [ { "name": "Principles and Frameworks of Research Integrity", diff --git a/layouts/clusters/cluster.html b/layouts/clusters/cluster.html index 3ded15724b6..dd6c960df2b 100644 --- a/layouts/clusters/cluster.html +++ b/layouts/clusters/cluster.html @@ -35,34 +35,36 @@ {{ else }} {{ partial "clusters/cluster_seo_jsonld.html" (dict "page" . "cluster" $cluster) }} - <div class="clusters-cluster-subpage"> - <div class="universal-wrapper pt-2 pb-0 clusters-cluster-subpage__head-wrap"> + {{/* Breadcrumb header — narrow width like main page title */}} + <div class="universal-wrapper pt-3 pb-2"> <div class="container"> - <div class="clusters-cluster-subpage__head-inner"> + <div class="article-container pt-3"> {{ $heading := .Params.heading_title | default .Title }} <nav aria-label="breadcrumb" class="clusters-heading-row__crumbs mb-1"> - <a href="{{ "/clusters/" | relURL }}" class="clusters-heading-row__parent">FORRT clusters</a> + <a href="{{ "/clusters/" | relURL }}" class="clusters-heading-row__parent">FORRT Clusters</a> <span class="clusters-heading-row__sep" aria-hidden="true">/</span> <h1 class="clusters-heading-row__title clusters-site-heading" itemprop="headline">{{ $heading }}</h1> </nav> - - <div class="clusters-title-toolbar"> - {{ partial "clusters/clusters_controls.html" . }} - </div> </div> </div> </div> - {{ $colors := slice "#cacfdc" "#eadce6" "#d4e4d9" "#BDC5CA" "#dce4ea" "#e8ddd4" "#c9dbcb" "#d9cfe0" "#cddde3" "#e0d8cc" "#d4dce8" }} - {{ $arrowColors := slice "#6070a0" "#a05080" "#408060" "#607080" "#5080a0" "#a08060" "#509060" "#8060a0" "#5090a0" "#907050" "#6070a0" }} + {{ $palette := partial "clusters/colors.html" }} + {{ $colors := $palette.colors }} + {{ $arrowColors := $palette.arrowColors }} {{ $ci := sub $n 1 }} - <section class="clusters-display-section clusters-cluster-subpage__display"> + {{/* Main content section — same structure as hub page */}} + <section class="cluster-full-width clusters-display-section"> <div class="container"> - <div class="clusters-layout clusters-layout--cluster-subpage"> - <div class="row clusters-cluster-subpage__row"> + <div class="clusters-layout"> + + {{ partial "clusters/clusters_controls.html" . }} + + <div class="row"> {{ partial "clusters/sidebar_nav.html" (dict "data" $data "arrowColors" $arrowColors "link_mode" "subpath" "active_cluster_number" $n) }} - <main class="col-12 col-lg-8 col-xl-9 clusters-content clusters-cluster-subpage__main-scroll"> + + <main class="col-12 col-lg-8 col-xl-9 clusters-content"> {{ with .Content }} <div class="article-container pt-2 pb-2"> <div class="article-style clusters-cluster-lead">{{ . }}</div> @@ -78,6 +80,5 @@ <h1 class="clusters-heading-row__title clusters-site-heading" itemprop="headline </button> </div> </section> - </div> {{ end }} {{ end }} diff --git a/layouts/clusters/list.html b/layouts/clusters/list.html deleted file mode 100644 index 2c31da27d70..00000000000 --- a/layouts/clusters/list.html +++ /dev/null @@ -1,45 +0,0 @@ -{{/* layouts/clusters/list.html - List layout for clusters section */}} -{{ define "main" }} - {{ partial "clusters/seo_jsonld.html" . }} - <div class="universal-wrapper pt-3 pb-3"> - <div class="container"> - - {{/* Clusters page header */}} - {{ if .Params.image }} - <div class="article-header d-print-none"> - <img src="{{ .Params.image }}" alt="{{ .Params.heading_title | default .Title }}" class="article-banner" loading="lazy"> - </div> - {{ end }} - - <div class="article-container pt-3"> - <h1 class="clusters-site-heading" itemprop="headline">{{ .Params.heading_title | default .Title }}</h1> - - {{/* Subtitle if present */}} - {{ if .Params.subtitle }} - <p class="page-subtitle">{{ .Params.subtitle | markdownify }}</p> - {{ end }} - - {{/* Optional section content */}} - {{ with .Content }} - <div class="article-style"> - {{ . }} - </div> - {{ end }} - </div> - </div> - </div> - - {{/* CLUSTERS INTRO SECTION */}} - <section class="clusters-intro-section"> - <div class="container"> - {{ partial "clusters/intro.html" . }} - </div> - </section> - - {{/* CLUSTERS DISPLAY SECTION */}} - <section class="clusters-display-section"> - <div class="container"> - {{ partial "clusters/all_clusters.html" . }} - </div> - </section> -{{ end }} diff --git a/layouts/partials/clusters/all_clusters.html b/layouts/partials/clusters/all_clusters.html index 5f2a1c8a793..20984a04a20 100644 --- a/layouts/partials/clusters/all_clusters.html +++ b/layouts/partials/clusters/all_clusters.html @@ -7,8 +7,9 @@ {{ return }} {{ end }} -{{ $colors := slice "#cacfdc" "#eadce6" "#d4e4d9" "#BDC5CA" "#dce4ea" "#e8ddd4" "#c9dbcb" "#d9cfe0" "#cddde3" "#e0d8cc" "#d4dce8" }} -{{ $arrowColors := slice "#6070a0" "#a05080" "#408060" "#607080" "#5080a0" "#a08060" "#509060" "#8060a0" "#5090a0" "#907050" "#6070a0" }} +{{ $palette := partial "clusters/colors.html" }} +{{ $colors := $palette.colors }} +{{ $arrowColors := $palette.arrowColors }} <div class="clusters-layout"> diff --git a/layouts/partials/clusters/clusters_controls.html b/layouts/partials/clusters/clusters_controls.html index b6c34483b0d..0a9413d31d7 100644 --- a/layouts/partials/clusters/clusters_controls.html +++ b/layouts/partials/clusters/clusters_controls.html @@ -7,6 +7,10 @@ <button type="button" class="btn btn-sm btn-primary clusters-inline-search__submit" id="clusters-inline-search-btn" aria-label="Run search"> <i class="fas fa-search" aria-hidden="true"></i> </button> + <label class="clusters-inline-search__option-label"> + <input type="checkbox" id="clusters-search-include-refs"> + Include references + </label> </div> <div id="clusters-inline-search-panel" class="clusters-inline-search__panel"> <div id="clusters-inline-search-toolbar" class="clusters-inline-search__toolbar-host" hidden></div> diff --git a/layouts/partials/clusters/colors.html b/layouts/partials/clusters/colors.html new file mode 100644 index 00000000000..8e1f9499114 --- /dev/null +++ b/layouts/partials/clusters/colors.html @@ -0,0 +1,4 @@ +{{/* Shared cluster color palettes — used by all_clusters.html and cluster.html */}} +{{ $colors := slice "#cacfdc" "#eadce6" "#d4e4d9" "#BDC5CA" "#dce4ea" "#e8ddd4" "#c9dbcb" "#d9cfe0" "#cddde3" "#e0d8cc" "#d4dce8" }} +{{ $arrowColors := slice "#6070a0" "#a05080" "#408060" "#607080" "#5080a0" "#a08060" "#509060" "#8060a0" "#5090a0" "#907050" "#6070a0" }} +{{ return dict "colors" $colors "arrowColors" $arrowColors }} diff --git a/layouts/partials/clusters/sidebar_nav.html b/layouts/partials/clusters/sidebar_nav.html index f8e20c824a2..fe4ca4298e3 100644 --- a/layouts/partials/clusters/sidebar_nav.html +++ b/layouts/partials/clusters/sidebar_nav.html @@ -1,4 +1,4 @@ -{{/* Sidebar: link_mode "anchor" (#cluster-N on hub) or "subpath" (/clusters/cluster-N/ on subpages). active_cluster_number highlights + expands that group on subpages. */}} +{{/* Sidebar: link_mode "anchor" (#cluster-N on hub) or "subpath" (/clusters/cluster-N/ on subpages). active_cluster_number pre-expands that group on subpages. */}} {{ $data := .data }} {{ $arrowColors := .arrowColors }} {{ $link_mode := .link_mode | default "anchor" }} @@ -6,24 +6,26 @@ <div class="col-lg-4 col-xl-3 clusters-sidebar" id="clusters-sidebar"> <div class="clusters-sidebar-inner"> - <div class="sidebar-header">{{ if eq $link_mode "subpath" }}Clusters{{ else }}Clusters & Sub-clusters{{ end }}</div> + <div class="sidebar-header">Clusters & Sub-clusters</div> <nav id="cluster-nav"> {{ range $ci, $cluster := $data.clusters }} {{ $cid := printf "cluster-%d" (int $cluster.number) }} {{ $cn := int $cluster.number }} {{ $isActive := eq $cn $activeN }} {{ $clusterHref := cond (eq $link_mode "subpath") (printf "/clusters/cluster-%d/" (int $cluster.number) | relURL) (printf "#%s" $cid) }} - <div class="cluster-nav-group{{ if $isActive }} cluster-nav-group--active{{ end }}" data-cluster="{{ $cid }}"> - <a href="{{ $clusterHref }}" class="cluster-nav-heading{{ if $isActive }} cluster-nav-heading--active{{ end }}"{{ if $isActive }} aria-current="page"{{ end }}> + <div class="cluster-nav-group" data-cluster="{{ $cid }}"> + <a href="{{ $clusterHref }}" class="cluster-nav-heading"{{ if $isActive }} aria-current="page"{{ end }}> {{ $arrowColor := index $arrowColors (mod $ci (len $arrowColors)) }} - <span class="cluster-nav-toggle" style="color:{{ $arrowColor }};">▸</span> + <span class="cluster-nav-toggle" style="color:{{ $arrowColor }};">{{ if $isActive }}▾{{ else }}▸{{ end }}</span> {{ $cluster.name }} </a> - <ul class="cluster-nav-subs" style="display:none;"> + <ul class="cluster-nav-subs" style="display:{{ if $isActive }}block{{ else }}none{{ end }};"> {{ range $si, $sc := $cluster.sub_clusters }} {{ $scid := printf "c%d-sc%d" (int $cluster.number) $si }} - {{/* Subpath: include pane hash so the target tab opens after navigation */}} - {{ $subHref := cond (eq $link_mode "subpath") (printf "/clusters/cluster-%d/#%s" (int $cluster.number) $scid | relURL) (printf "#%s" $cid) }} + {{ $subHref := printf "#%s" $cid }} + {{ if and (eq $link_mode "subpath") (not $isActive) }} + {{ $subHref = printf "/clusters/cluster-%d/#%s" (int $cluster.number) $scid | relURL }} + {{ end }} <li class="nav-item"> <a href="{{ $subHref }}" class="nav-link sc-nav-link" data-cluster="{{ $cid }}" data-tab="{{ $scid }}-tab"> {{ $sc.name }} diff --git a/static/js/clusters-page.js b/static/js/clusters-page.js index c5dacd2a9df..c6403222ff4 100644 --- a/static/js/clusters-page.js +++ b/static/js/clusters-page.js @@ -86,7 +86,7 @@ } } - function collectClustersInlineSearchResults(scopeRoot, tokens) { + function collectClustersInlineSearchResults(scopeRoot, tokens, includeRefs) { var results = []; var seen = {}; @@ -136,6 +136,26 @@ meta: clusterName }); } + + if (includeRefs) { + pane.querySelectorAll('.publication-item').forEach(function (pubEl, pi) { + if (results.length >= MAX_RESULTS) return; + var pubText = pubEl.textContent.replace(/\s+/g, ' ').trim(); + if (!pubText) return; + if (matchesAllTokens(pubText, tokens)) { + var truncated = pubText.length > 120 ? pubText.substring(0, 120) + '…' : pubText; + add('pub:' + clusterId + ':' + paneId + ':' + pi, { + type: 'publication', + clusterId: clusterId, + tabId: tabId, + paneId: paneId, + pubIndex: pi, + label: truncated, + meta: scName + }); + } + }); + } }); }); @@ -166,6 +186,11 @@ return; } + /* Sort: clusters & sub-clusters first, then publications */ + results.sort(function (a, b) { + var order = { cluster: 0, subcluster: 1, publication: 2 }; + return (order[a.type] || 9) - (order[b.type] || 9); + }); var shown = results.slice(0, SHOWN_RESULTS); var countText = results.length + ' result' + (results.length !== 1 ? 's' : ''); toolbarEl.innerHTML = buildResultsToolbar(countText); @@ -173,14 +198,21 @@ var html = '<div class="clusters-inline-search__hits">'; shown.forEach(function (r) { - html += '<a href="#" class="clusters-inline-search__hit" role="button"' + + var extraAttr = r.pubIndex != null ? ' data-pub-index="' + escAttr(r.pubIndex) + '"' : ''; + var isPub = r.type === 'publication'; + var icon = isPub ? '<i class="fas fa-file-alt clusters-inline-search__hit-icon" aria-hidden="true"></i>' : ''; + var hitClass = 'clusters-inline-search__hit' + (isPub ? ' clusters-inline-search__hit--publication' : ''); + html += '<a href="#" class="' + hitClass + '" role="button"' + ' data-hit-type="' + escAttr(r.type) + '"' + ' data-cluster="' + escAttr(r.clusterId) + '"' + ' data-tab="' + escAttr(r.tabId) + '"' + - ' data-pane="' + escAttr(r.paneId) + '">' + + ' data-pane="' + escAttr(r.paneId) + '"' + + extraAttr + '>' + + icon + + '<span class="clusters-inline-search__hit-text">' + '<span class="clusters-inline-search__hit-label">' + escapeHtml(r.label) + '</span>' + '<span class="clusters-inline-search__hit-meta">' + escapeHtml(r.meta) + '</span>' + - '</a>'; + '</span></a>'; }); html += '</div>'; @@ -202,69 +234,13 @@ var controls = document.querySelector('.clusters-controls'); var navbarEl = document.getElementById('navbar-main'); var mobileNavMq = window.matchMedia ? window.matchMedia('(max-width: 991.98px)') : null; - var clusterSubpage = document.querySelector('.clusters-cluster-subpage'); - var mainScrollEl = document.querySelector('.clusters-cluster-subpage__main-scroll'); function clustersNavIsMobileWidth() { return mobileNavMq && mobileNavMq.matches; } - /** /clusters/cluster-N/: desktop main column is the scroll container */ - function useClusterSubpageMainScroll() { - if (!clusterSubpage || !mainScrollEl) return false; - if (clustersNavIsMobileWidth()) return false; - var oy = window.getComputedStyle(mainScrollEl).overflowY; - return oy === 'auto' || oy === 'scroll'; - } - - function updateClusterSubpageDrawerTop() { - if (!clusterSubpage || !clustersNavIsMobileWidth()) { - document.documentElement.style.removeProperty('--cluster-subpage-drawer-top'); - return; - } - var bar = clusterSubpage.querySelector('.clusters-cluster-subpage__head-wrap'); - if (bar) { - document.documentElement.style.setProperty( - '--cluster-subpage-drawer-top', - Math.ceil(bar.getBoundingClientRect().bottom) + 4 + 'px' - ); - } - } - - function updateClusterSubpageLayout() { - if (!clusterSubpage) { - document.documentElement.style.removeProperty('--cluster-subpage-sticky-top'); - document.documentElement.style.removeProperty('--cluster-subpage-drawer-top'); - return; - } - var navOff = getNavbarStickyOffsetPx(); - clusterSubpage.style.setProperty('--cluster-subpage-nav-offset', navOff + 'px'); - document.documentElement.style.setProperty( - '--cluster-subpage-sticky-top', - 'calc(' + navOff + 'px + env(safe-area-inset-top, 0px))' - ); - if (clustersNavIsMobileWidth()) { - clusterSubpage.style.removeProperty('--cluster-subpage-head-reserved'); - updateClusterSubpageDrawerTop(); - return; - } - document.documentElement.style.removeProperty('--cluster-subpage-drawer-top'); - var display = clusterSubpage.querySelector('.clusters-cluster-subpage__display'); - if (display) { - clusterSubpage.style.setProperty( - '--cluster-subpage-head-reserved', - Math.ceil(display.getBoundingClientRect().top) + 12 + 'px' - ); - } - } - - /** Hub: lock body when drawer open. Cluster subpage: dropdown below bar — keep page scroll. */ function syncClustersMobileBodyScrollLock() { if (!sidebar) return; - if (clusterSubpage && clustersNavIsMobileWidth()) { - document.body.style.overflow = ''; - return; - } if (!clustersNavIsMobileWidth() || !sidebar.classList.contains('sidebar-open')) { document.body.style.overflow = ''; } else { @@ -284,15 +260,16 @@ '--clusters-controls-height', controls ? controls.offsetHeight + 'px' : '0px' ); + /* Keep tab content tall enough so the footer stays below the fold */ + var vh = window.innerHeight + 'px'; + root.querySelectorAll('.cluster-tab-content').forEach(function (tc) { + tc.style.minHeight = vh; + }); } function scheduleStickyLayoutMetrics() { updateStickyLayoutMetrics(); - updateClusterSubpageLayout(); - requestAnimationFrame(function () { - updateStickyLayoutMetrics(); - updateClusterSubpageLayout(); - }); + requestAnimationFrame(updateStickyLayoutMetrics); } scheduleStickyLayoutMetrics(); @@ -318,18 +295,11 @@ if (window.ResizeObserver && controls) { new ResizeObserver(scheduleStickyLayoutMetrics).observe(controls); } - if (window.ResizeObserver && clusterSubpage) { - new ResizeObserver(scheduleStickyLayoutMetrics).observe(clusterSubpage); - } - /** - * Scroll so el sits below the sticky stack (navbar + .clusters-controls search bar). - * Cluster subpages: scroll the <main> column only (desktop). - */ + /** Scroll so el sits below the sticky stack (navbar + .clusters-controls search bar). */ function scrollElementBelowStickyChrome(el) { if (!el) return; updateStickyLayoutMetrics(); - updateClusterSubpageLayout(); requestAnimationFrame(function () { requestAnimationFrame(function () { var margin = 14; @@ -340,11 +310,6 @@ var navbar = document.getElementById('navbar-main'); chromeBottom = navbar ? Math.ceil(navbar.getBoundingClientRect().bottom) : 72; } - if (useClusterSubpageMainScroll() && mainScrollEl) { - var delta = el.getBoundingClientRect().top - chromeBottom - margin; - mainScrollEl.scrollBy({ top: delta, behavior: 'smooth' }); - return; - } var elTopDoc = el.getBoundingClientRect().top + window.pageYOffset; var targetScroll = elTopDoc - chromeBottom - margin; window.scrollTo({ top: Math.max(0, targetScroll), behavior: 'smooth' }); @@ -376,44 +341,41 @@ sidebar.classList.toggle('sidebar-open'); this.classList.toggle('active'); scheduleStickyLayoutMetrics(); - requestAnimationFrame(function () { - updateClusterSubpageDrawerTop(); - syncClustersMobileBodyScrollLock(); - }); + requestAnimationFrame(syncClustersMobileBodyScrollLock); }); } - if (clusterSubpage) { - window.addEventListener( - 'scroll', - function () { - if (clustersNavIsMobileWidth() && sidebar && sidebar.classList.contains('sidebar-open')) { - updateClusterSubpageDrawerTop(); - } - }, - { passive: true } - ); - } - root.querySelectorAll('.cluster-nav-heading').forEach(function (heading) { heading.addEventListener('click', function (e) { - /* /clusters/cluster-N/ links: navigate; #cluster-N on hub: expand + scroll in-page */ + var clickedArrow = e.target.closest('.cluster-nav-toggle'); + var group = this.closest('.cluster-nav-group'); + if (!group) return; + var subList = group.querySelector('.cluster-nav-subs'); + var arrow = group.querySelector('.cluster-nav-toggle'); + + /* Arrow click: always toggle expand/collapse, never navigate */ + if (clickedArrow) { + e.preventDefault(); + if (!subList || !arrow) return; + var isHidden = subList.style.display === 'none'; + subList.style.display = isHidden ? 'block' : 'none'; + arrow.innerHTML = isHidden ? '▾' : '▸'; + return; + } + + /* Text click on subpath links: navigate to that cluster page */ if (!isClustersInPageNavHref(this)) { closeClustersMobileSidebar(); return; } + + /* Text click on in-page anchor links: expand + scroll */ e.preventDefault(); - var group = this.closest('.cluster-nav-group'); - if (!group) return; - var subList = group.querySelector('.cluster-nav-subs'); - var arrow = group.querySelector('.cluster-nav-toggle'); - if (!subList || !arrow) return; - var isHidden = subList.style.display === 'none'; - subList.style.display = isHidden ? 'block' : 'none'; - arrow.innerHTML = isHidden ? '▾' : '▸'; - /* Arrow: expand/collapse only — keep mobile drawer open for sub-cluster picks */ - var clickedArrow = e.target.closest('.cluster-nav-toggle'); - if (clickedArrow) return; + if (subList && arrow) { + var isHidden = subList.style.display === 'none'; + subList.style.display = isHidden ? 'block' : 'none'; + arrow.innerHTML = isHidden ? '▾' : '▸'; + } var clusterId = group.getAttribute('data-cluster'); var section = clusterId ? document.getElementById(clusterId) : null; if (section) { @@ -526,12 +488,22 @@ hideSearchResults(); return; } - var results = collectClustersInlineSearchResults(root, tokens); + var includeRefsEl = document.getElementById('clusters-search-include-refs'); + var includeRefs = includeRefsEl ? includeRefsEl.checked : false; + var results = collectClustersInlineSearchResults(root, tokens, includeRefs); renderClustersInlineResults(results, searchToolbar, searchResults); searchPanel.classList.add(RESULTS_OPEN_CLASS); scheduleStickyLayoutMetrics(); } + var includeRefsCheckbox = document.getElementById('clusters-search-include-refs'); + if (includeRefsCheckbox) { + includeRefsCheckbox.addEventListener('change', function () { + clearTimeout(debounceTimer); + runInlineSearch(); + }); + } + if (searchInput && searchResults && searchPanel && searchToolbar) { searchInput.addEventListener('input', function () { clearTimeout(debounceTimer); @@ -591,6 +563,15 @@ section.querySelector('.cluster-header') || section.querySelector('.cluster-title') || section; + } else if (hitType === 'publication' && paneId) { + var panePub = document.getElementById(paneId); + var pubIdx = parseInt(link.getAttribute('data-pub-index'), 10); + if (panePub && !isNaN(pubIdx)) { + var pubs = panePub.querySelectorAll('.publication-item'); + scrollEl = pubs[pubIdx] || panePub; + } else { + scrollEl = panePub || section; + } } else if (hitType === 'subcluster' && paneId) { var paneSc = document.getElementById(paneId); scrollEl = paneSc ? paneSc.querySelector('.sc-heading') || paneSc : section; @@ -620,21 +601,12 @@ if (backToTopBtn) { function toggleBackToTop() { - var useMain = useClusterSubpageMainScroll(); - var show = useMain ? mainScrollEl.scrollTop > 400 : window.scrollY > 500; - backToTopBtn.classList.toggle('is-visible', show); + backToTopBtn.classList.toggle('is-visible', window.scrollY > 500); } window.addEventListener('scroll', toggleBackToTop, { passive: true }); - if (mainScrollEl) { - mainScrollEl.addEventListener('scroll', toggleBackToTop, { passive: true }); - } toggleBackToTop(); backToTopBtn.addEventListener('click', function () { - if (useClusterSubpageMainScroll() && mainScrollEl) { - mainScrollEl.scrollTo({ top: 0, behavior: 'smooth' }); - } else { - window.scrollTo({ top: 0, behavior: 'smooth' }); - } + window.scrollTo({ top: 0, behavior: 'smooth' }); }); } });