style: standardized citation format across modules

lter · Aug 28, 2024 · 6f5a1e7 · 6f5a1e7
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diff --git a/_freeze/mod_data-viz/execute-results/html.json b/_freeze/mod_data-viz/execute-results/html.json
diff --git a/_freeze/mod_data-viz/figure-html/multi-modal-1.png b/_freeze/mod_data-viz/figure-html/multi-modal-1.png
diff --git a/_freeze/mod_data-viz/figure-html/nms-ord-1.png b/_freeze/mod_data-viz/figure-html/nms-ord-1.png
diff --git a/_freeze/mod_interactivity/execute-results/html.json b/_freeze/mod_interactivity/execute-results/html.json
diff --git a/_freeze/mod_reports/execute-results/html.json b/_freeze/mod_reports/execute-results/html.json
diff --git a/_freeze/mod_spatial/execute-results/html.json b/_freeze/mod_spatial/execute-results/html.json
diff --git a/_freeze/mod_stats/execute-results/html.json b/_freeze/mod_stats/execute-results/html.json
diff --git a/_freeze/mod_stats/figure-html/mem-explore-graph-1.png b/_freeze/mod_stats/figure-html/mem-explore-graph-1.png
diff --git a/_freeze/mod_wrangle/execute-results/html.json b/_freeze/mod_wrangle/execute-results/html.json
diff --git a/mod_credit.qmd b/mod_credit.qmd
@@ -23,9 +23,9 @@ After completing this module you will be able to:
 
 ### Papers & Documents
 
-- Puebla _et al._ [Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012296). **2024**. _PLoS Computational Biology_
-- Dahlin _et al._, [Hear Every Voice, Working Groups that Work](https://esajournals.onlinelibrary.wiley.com/doi/10.1002/fee.2115). **2019**. _Frontiers in Ecology and the Environment_
-- Allen _et al._, [How Can We Ensure Visibility and Diversity in Research Contributions? How the Contributor Role Taxonomy (CReDiT) is Helping the Shift from Authorship to Contributorship](https://onlinelibrary.wiley.com/doi/epdf/10.1002/leap.1210). **2018**. _Learned Publishing_
+- Puebla, I. _et al._ [Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012296). **2024**. _PLoS Computational Biology_
+- Dahlin, K.M. _et al._, [Hear Every Voice, Working Groups that Work](https://esajournals.onlinelibrary.wiley.com/doi/10.1002/fee.2115). **2019**. _Frontiers in Ecology and the Environment_
+- Allen, L. _et al._, [How Can We Ensure Visibility and Diversity in Research Contributions? How the Contributor Role Taxonomy (CReDiT) is Helping the Shift from Authorship to Contributorship](https://onlinelibrary.wiley.com/doi/epdf/10.1002/leap.1210). **2018**. _Learned Publishing_
 
 ### Workshops & Courses
 

diff --git a/mod_data-disc.qmd b/mod_data-disc.qmd
@@ -25,14 +25,14 @@ After completing this module you will be able to:
 
 ### Papers & Documents
 
-- The British Ecological Society's [Better Science Guides](https://www.britishecologicalsociety.org/publications/better-science/) -- Data Management Guide
+- British Ecological Society (BES). [Better Science Guides: Data Management Guide ](https://www.britishecologicalsociety.org/publications/better-science/). **2024**.
 
 ### Workshops & Courses
 
-- NCEAS coreR [Data Management Essentials](https://learning.nceas.ucsb.edu/2023-10-coreR/session_14.html) lesson
-- Open Science Synthesis for the Delta Science Program's [Data Management Essentials and the FAIR & CARE Principles](https://learning.nceas.ucsb.edu/2023-09-ucsb-faculty/session_04.html)
-- Open Science Synthesis for the Delta Science Program's [Writing Data Management Plans](https://learning.nceas.ucsb.edu/2023-09-ucsb-faculty/session_05.html)
-- NCEAS Scientific Computing team's [Data Acquisition](https://nceas.github.io/scicomp.github.io/data-acquisition.html) instructions
+- LTER Scientific Computing Team. [Data Acquisition Guide for TRY and AppEEARS](https://lter.github.io/scicomp/internal_get-data.html). **2024**.
+- National Center for Ecological Analysis and Synthesis (NCEAS) Learning Hub. [coreR: Data Management Essentials](https://learning.nceas.ucsb.edu/2023-10-coreR/session_14.html). **2023**.
+- NCEAS Learning Hub. [UCSB Faculty Seminar Series: Data Management Essentials and the FAIR & CARE Principles](https://learning.nceas.ucsb.edu/2023-09-ucsb-faculty/session_04.html). **2023**.
+- NCEAS Learning Hub. [UCSB Faculty Seminar Series: Writing Data Management Plans](https://learning.nceas.ucsb.edu/2023-09-ucsb-faculty/session_05.html). **2023**.
 
 ### Websites
 

diff --git a/mod_data-viz.qmd b/mod_data-viz.qmd
@@ -565,13 +565,13 @@ Check out the [bonus spatial data module](https://lter.github.io/ssecr/mod_spati
 
 ### Papers & Documents
 
-- NCEAS [Colorblind Safe Color Schemes](https://www.nceas.ucsb.edu/sites/default/files/2022-06/Colorblind%20Safe%20Color%20Schemes.pdf) reference document
+- National Center for Ecological Analysis and Synthesis (NCEAS). [Colorblind Safe Color Schemes](https://www.nceas.ucsb.edu/sites/default/files/2022-06/Colorblind%20Safe%20Color%20Schemes.pdf). **2022**.
 
 ### Workshops & Courses
 
-- NCEAS Scientific Computing team's Coding in the Tidyverse workshop [`ggplot2` module](https://nceas.github.io/scicomp-workshop-tidyverse/visualize.html)
-- The Carpentries' Data Analysis and Visualization in R for Ecologists [`ggplot2` episode](https://datacarpentry.org/R-ecology-lesson/04-visualization-ggplot2.html)
-
+- The Carpentries. [Data Analysis and Visualization in R for Ecologists: Data Visualization with `ggplot2`](https://datacarpentry.org/R-ecology-lesson/visualizing-ggplot.html). **2024**.
+- The Carpentries. [Data Analysis and Visualization in Python for Ecologists: Making Plots with `plotnine`](https://datacarpentry.org/python-ecology-lesson/07-visualization-ggplot-python.html). **2024**.
+- LTER Scientific Computing Team. [Coding in the Tidyverse: 'Visualize' Module](https://lter.github.io/workshop-tidyverse/visualize.html). **2023**.
 
 ### Websites
 

diff --git a/mod_facilitation.qmd b/mod_facilitation.qmd
@@ -23,12 +23,12 @@ After completing this module you will be able to:
 
 ### Papers & Documents
 
-- _[Facilitator's Guide to Participatory Decision-Making](https://bookshop.org/p/books/facilitator-s-guide-to-participatory-decision-making-sam-kaner/11179446?ean=9781118404959)_ by Sam Kaner
+- Kaner, S. [Facilitator's Guide to Participatory Decision-Making (Revised)](https://bookshop.org/p/books/facilitator-s-guide-to-participatory-decision-making-sam-kaner/11179446?ean=9781118404959). **2014**.
 
 ### Workshops & Courses
 
 - 
 
 ### Websites
 
-- [Liberating Structures](https://www.liberatingstructures.com/) website
+- [Liberating Structures: Including and Uleashing Everyone](https://www.liberatingstructures.com/)
diff --git a/mod_findings.qmd b/mod_findings.qmd
@@ -35,8 +35,9 @@ After completing this module you will be able to:
 
 ### Workshops & Courses
 
-- Open Science Synthesis for the Delta Science Program's [Communicating Your Science](https://learning.nceas.ucsb.edu/2023-10-delta/session_02.html)
+
+- NCEAS Learning Hub & Delta Stewardship Council. [Open Science Synthesis: Communicating Your Science ](https://learning.nceas.ucsb.edu/2023-10-delta/session_02.html). **2023**.
 
 ### Websites
 
-- Compass' [The Message Box](https://www.compassscicomm.org/leadership-development/the-message-box/)
+- COMPASS. [The Message Box](https://www.compassscicomm.org/leadership-development/the-message-box/)
diff --git a/mod_interactivity.qmd b/mod_interactivity.qmd
@@ -330,9 +330,9 @@ Take a look at [Posit's instructions for deployment](https://shiny.posit.co/r/ar
 
 ### Workshops & Courses
 
-- Posit's [Welcome to Shiny](https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html) (for R coders)
-- 2022 All Scientists' Meeting [Shiny Apps for Sharing Science](https://njlyon0.github.io/asm-2022_shiny-workshop/) workshop
+- Posit. [Welcome to Shiny](https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html). **2024**.
+- Lyon, N.J., _et al._ [Shiny Apps for Sharing Science](https://njlyon0.github.io/asm-2022_shiny-workshop/). **2022**.
 
 ### Websites
 
-- Posit's [Shiny](https://shiny.posit.co/) website
+- 
diff --git a/mod_next-steps.qmd b/mod_next-steps.qmd
@@ -22,12 +22,12 @@ After completing this module you will be able to:
 
 ### Papers & Documents
 
-- Deutsch _et al._, [Leading Inter- and Transdisciplinary Research: Lessons from Applying Theories of Change to a Strategic Research Program](https://www.sciencedirect.com/science/article/pii/S146290112100054X?via%3Dihub). **2021**. _Environmental Science & Policy_
+- Deutsch L., _et al._, [Leading Inter- and Transdisciplinary Research: Lessons from Applying Theories of Change to a Strategic Research Program](https://www.sciencedirect.com/science/article/pii/S146290112100054X?via%3Dihub). **2021**. _Environmental Science & Policy_
 
 ### Workshops & Courses
 
 - 
 
 ### Websites
 
-- Shabanov, I. (\@Artifexx) [X post on logic models](https://x.com/artifexx/status/1798936726788051403?s=51&t=TCar5jaRTW3NNuD_rXT8Pg)
+- Shabanov, I. (\@Artifexx) [Tweet on logic models](https://x.com/artifexx/status/1798936726788051403?s=51&t=TCar5jaRTW3NNuD_rXT8Pg). **2024**.
diff --git a/mod_project-mgmt.qmd b/mod_project-mgmt.qmd
@@ -27,10 +27,10 @@ After completing this module you will be able to:
 
 ### Workshops & Courses
 
-- NCEAS Scientific Computing team's Collaborative Coding with GitHub workshop project management modules
-    - [GitHub Issues](https://nceas.github.io/scicomp-workshop-collaborative-coding/issues.html)
-    - [GitHub Projects](https://nceas.github.io/scicomp-workshop-collaborative-coding/projects.html)
-- Open Science Synthesis for the Delta Science Program's [Logic Models and Synthesis Development](https://learning.nceas.ucsb.edu/2021-09-delta/session-8-hands-on-logic-models-and-synthesis-development.html)
+- LTER Scientific Computing Team. [Collaborative Coding with GitHub: Issues](https://lter.github.io/workshop-github/issues.html). **2024**.
+- LTER Scientific Computing Team. [Collaborative Coding with GitHub: Milestones](https://lter.github.io/workshop-github/milestones.html). **2024**.
+- LTER Scientific Computing Team. [Collaborative Coding with GitHub: Projects](https://lter.github.io/workshop-github/projects.html). **2024**.
+- NCEAS Learning Hub & Delta Stewardship Council. [Open Science Synthesis: Logic Models and Synthesis Development](https://learning.nceas.ucsb.edu/2021-09-delta/session-8-hands-on-logic-models-and-synthesis-development.html). **2021**.
 
 ### Websites
 

diff --git a/mod_reports.qmd b/mod_reports.qmd
@@ -121,11 +121,10 @@ See [here](https://nceas.github.io/scicomp.github.io/best_practices.html#r-scrip
 
 ### Workshops & Courses
 
-- NCEAS coreR [Literate Analysis with Quarto](https://learning.nceas.ucsb.edu/2023-10-coreR/session_04.html) session
-- OSS [Reproducible Papers with RMarkdown](https://nceas.github.io/oss-lessons/reproducible-papers-with-rmd/reproducible-papers-with-rmd.html)
-- UCSB's Master of Environmental Data Science (MEDS) [Creating your Personal Website using Quarto](https://ucsb-meds.github.io/creating-quarto-websites/) lesson
+- Csik, S. [Creating Your Personal Website Using Quarto](https://ucsb-meds.github.io/creating-quarto-websites/). **2024**.
+- National Center for Ecological Analysis and Synthesis (NCEAS) Learning Hub. [coreR: Literate Analysis with Quarto](https://learning.nceas.ucsb.edu/2023-10-coreR/session_04.html). **2023**.
+- Mecum, B. [Reproducible Papers with RMarkdown](https://nceas.github.io/oss-lessons/reproducible-papers-with-rmd/reproducible-papers-with-rmd.html). **2019**.
 
 ### Websites
-
-- Markdown Guide: [Basic Syntax](https://www.markdownguide.org/basic-syntax/)
-- Posit's [Welcome to Quarto](https://quarto.org/)
+- [The Markdown Guide: Basic Syntax](https://www.markdownguide.org/basic-syntax/).
+- Posit. [Welcome to Quarto](https://quarto.org/)
diff --git a/mod_reproducibility.qmd b/mod_reproducibility.qmd
@@ -578,24 +578,23 @@ Making sure that your project is reproducible requires a handful of steps before
 
 ### Papers & Documents
 
-- [A Large-Scale Study on Research Code Quality and Execution](https://www.nature.com/articles/s41597-022-01143-6). Trisovic _et al._, 2022. **Scientific Data**
-- [Applying the 'CARE Principles for Indigenous Data Governance' to Ecology and Biodiversity Research](https://www.nature.com/articles/s41559-023-02161-2). Jennings _et al._, 2023. **Nature Ecology & Evolution**
-- [Guides to Better Science - Reproducible Code](https://www.britishecologicalsociety.org/publications/better-science/). The British Ecological Society, 2024.
-- [FAIR Teaching Handbook](https://fairsfair.gitbook.io/fair-teaching-handbook/). Englehardt _et al._, 2024.
-- [R Packages](https://r-pkgs.org/) (2nd ed.). Wickham & Bryan.
+- British Ecological Society (BES). [Better Science Guides: Reproducible Code](https://www.britishecologicalsociety.org/publications/better-science/). **2024**.
+- Englehardt, C. _et al._ [FAIR Teaching Handbook](https://fairsfair.gitbook.io/fair-teaching-handbook/). **2024**.
+- Jennings, L. _et al._ [Applying the 'CARE Principles for Indigenous Data Governance' to Ecology and Biodiversity Research](https://www.nature.com/articles/s41559-023-02161-2). **2023**. _Nature Ecology & Evolution_
+- Wickham, H. & Bryan, J. [R Packages](https://r-pkgs.org/) (2nd ed.). **2023**.
+- Trisovic, A. _et al._ [A Large-Scale Study on Research Code Quality and Execution](https://www.nature.com/articles/s41597-022-01143-6). **2022**. _Scientific Data_
 
 ### Workshops & Courses
 
-- Data Analysis and Visualization in R for Ecologists, [Episode 1: Before We Start](https://datacarpentry.org/R-ecology-lesson/00-before-we-start.html). The Carpentries
-- Introduction to R for Geospatial Data, [Episode 2: Project Management with RStudio](https://datacarpentry.org/r-intro-geospatial/02-project-intro.html). The Carpentries
-- coreR Course, [Chapter 5: FAIR and CARE Principles](https://learning.nceas.ucsb.edu/2023-10-coreR/session_05.html). National Center for Ecological Analysis and Synthesis (NCEAS) Learning Hub, 2023.
-- coreR Course, [Chapter 18: Reproducibility & Provenance](https://learning.nceas.ucsb.edu/2023-10-coreR/session_18.html). NCEAS Learning Hub, 2023.
+- The Carpentries. [Data Analysis and Visualization in R for Ecologists: Before We Start](https://datacarpentry.org/R-ecology-lesson/00-before-we-start.html). **2024**.
+- The Carpentries. [Introduction to R for Geospatial Data: Project Management with RStudio](https://datacarpentry.org/r-intro-geospatial/02-project-intro.html). **2024**.
+- National Center for Ecological Analysis and Synthesis (NCEAS) Learning Hub. [coreR: FAIR and CARE Principles](https://learning.nceas.ucsb.edu/2023-10-coreR/session_05.html). **2023**.
+- National Center for Ecological Analysis and Synthesis (NCEAS) Learning Hub. [coreR: Reproducibility & Provenance](https://learning.nceas.ucsb.edu/2023-10-coreR/session_18.html). **2023**.
 
 ### Websites
 
-- [Coding Tips](https://nceas.github.io/scicomp.github.io/best_practices.html). NCEAS Scientific Computing Team, 2024.
-- [Documenting Things: Openly for Future Us](https://openscapes.github.io/documenting-things/#/title-slide). Lowndes _et al.,_ 2023.
-- [Team Coding: 5 Essentials](https://nceas.github.io/scicomp.github.io/onboard-scaffold_team_coding.html). NCEAS Scientific Computing Team, 2024.
-- Advanced R (1st ed.) [Style Guide](http://adv-r.had.co.nz/Style.html). Wickham
-- PEP 8 [Style Guide for Python Code](https://peps.python.org/pep-0008/). van Rossum _et al._ 2013.
-- [Google Style Guides](https://google.github.io/styleguide/)
+- Google. [Style Guide](http://adv-r.had.co.nz/Style.html). **2024**.
+- LTER Scientific Computing Team. [Team Coding: 5 Essentials](https://lter.github.io/scicomp/wg_team-coding.html). **2024**.
+- Lowndes, J.S. _et al._ [Documenting Things: Openly for Future Us](https://openscapes.github.io/documenting-things/#/title-slide). **2023**. _posit::conf(2023)_
+- Wickham, H. [Advanced R: Style Guide](http://adv-r.had.co.nz/Style.html). (1st ed.). **2019**.
+- van Rossum, G. _et al._ [PEP 8: Style Guide for Python Code](https://peps.python.org/pep-0008/). **2013**. _Python Enhancement Proposals_
diff --git a/mod_spatial.qmd b/mod_spatial.qmd
@@ -297,12 +297,12 @@ In the above output we can see that it has extracted the elevation of _every pix
 
 ### Workshops & Courses
 
-- The Carpentries' [Introduction to Geospatial Raster & Vector Data with R](https://datacarpentry.org/r-raster-vector-geospatial/)
-- The Carpentries' [Introduction to R for Geospatial Data](https://datacarpentry.org/r-intro-geospatial/index.html)
-- Arctic Data Center's [Spatial and Image Data Using GeoPandas](https://learning.nceas.ucsb.edu/2023-03-arctic/sections/geopandas.html) chapter of their Scalable Computing course
-- Jason Flower's (UC Santa Barbara) [Introduction to rasters with `terra`](https://jflowernet.github.io/intro-terra-ecodatascience/)
-- King, R. [Spatial Data Visualization](https://github.com/king0708/spatial-data-viz) workshop
+- The Carpentries. [Introduction to Geospatial Raster and Vector Data with R](https://datacarpentry.org/r-raster-vector-geospatial/). **2024**.
+- The Carpentries. [Introduction to R for Geospatial Data](https://datacarpentry.org/r-intro-geospatial/index.html). **2024**.
+- King, R. [Spatial Data Visualization](https://github.com/king0708/spatial-data-viz). **2024**.
+- Flower, J. [Introduction to Rasters with `terra`](https://jflowernet.github.io/intro-terra-ecodatascience/). **2024**.
+- Clark, S.J., _et al._ [Spatial and Image Data Using GeoPandas](https://learning.nceas.ucsb.edu/2023-03-arctic/sections/geopandas.html). **2023**.
 
 ### Websites
 
-- NASA's <u>App</u>lication for <u>E</u>xtracting and <u>E</u>xploring <u>A</u>nalysis <u>R</u>eady <u>S</u>amples [(AppEEARS) Portal](https://appeears.earthdatacloud.nasa.gov/)
+- NASA. [AppEEARS Portal](https://appeears.earthdatacloud.nasa.gov/)
diff --git a/mod_stats.qmd b/mod_stats.qmd
@@ -337,18 +337,18 @@ After you've calculated all relevant effect sizes--using your chosen flavor of e
 
 ### Papers & Documents
 
-- [Understanding ‘It Depends’ in Ecology: A Guide to Hypothesising, Visualising and Interpreting Statistical Interactions](https://onlinelibrary.wiley.com/doi/10.1111/brv.12939). Spake _et al._, 2023. **Biological Reviews** 
-- [Improving Quantitative Synthesis to Achieve Generality in Ecology](https://www.nature.com/articles/s41559-022-01891-z). Spake _et al._, 2022.**Nature Ecology and Evolution**
-- [Doing Meta-Analysis with R: A Hands-On Guide](https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/). Harrier _et al._ 2023.
-- [Mixed Effects Models and Extensions in Ecology with R](https://link.springer.com/book/10.1007/978-0-387-87458-6). Zuur _et al._, 2009.
+- Spake, R. _et al._ [Understanding 'It Depends' in Ecology: A Guide to Hypothesising, Visualising and Interpreting Statistical Interactions](https://onlinelibrary.wiley.com/doi/10.1111/brv.12939). **2023**. _Biological Reviews_
+- Spake, R. _et al._ [Improving Quantitative Synthesis to Achieve Generality in Ecology](https://www.nature.com/articles/s41559-022-01891-z). **2022**. _Nature Ecology and Evolution_
+- Harrier, M. _et al._ [Doing Meta-Analysis with R: A Hands-On Guide](https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/). **2021**.
+- Zuur, A.F. _et al._ [Mixed Effects Models and Extensions in Ecology with R](https://link.springer.com/book/10.1007/978-0-387-87458-6). **2009**.
 
 ### Workshops & Courses
 
-- Matt Vuorre's [Bayesian Meta-Analysis with R, Stan, and brms](https://mvuorre.github.io/posts/2016-09-29-bayesian-meta-analysis/)
+- Vuorre, M. [Bayesian Meta-Analysis with R, Stan, and brms](https://mvuorre.github.io/posts/2016-09-29-bayesian-meta-analysis/). **2016**.
 
 ### Websites
 
-- [Bayesian Meta-Analysis in brms-II](https://solomonkurz.netlify.app/blog/2020-10-16-bayesian-meta-analysis-in-brms-ii/). Solomon Kurz, A., 2022.
-- [Meta-Analysis with R](https://github.com/wviechtb/workshop_2022_ma_esmarconf/blob/master/workshop_meta-analysis.pdf) slide deck. Viechtbauer, W., 2022.
-- [The `metafor` Package: A Meta-Analysis Package for R](https://www.metafor-project.org/doku.php/tips:rma_vs_lm_lme_lmer?s%5B%5D=lme4). Viechtbauer, W., 2021.
-- [Bayesian Meta-Analysis in brms](https://solomonkurz.netlify.app/blog/bayesian-meta-analysis/). Solomon Kurz, A., 2018.
+- Kurz, A. S. [Bayesian Meta-Analysis in brms-II](https://solomonkurz.netlify.app/blog/2020-10-16-bayesian-meta-analysis-in-brms-ii/). **2022**.
+- Viechtbauer, W. [Meta-Analysis with R](https://github.com/wviechtb/workshop_2022_ma_esmarconf/blob/master/workshop_meta-analysis.pdf). **2022**.
+- Viechtbauer, W. [The `metafor` Package: A Meta-Analysis Package for R](https://www.metafor-project.org/doku.php/tips:rma_vs_lm_lme_lmer?s%5B%5D=lme4). **2021**.
+- Kurz, A. S. [Bayesian Meta-Analysis in brms](https://solomonkurz.netlify.app/blog/bayesian-meta-analysis/). **2020**.