Merge pull request #39 from carpentries-incubator/ucsbcarpentry/main

merge in changes from UCSB Carpentry repo with updates for Quarto

.github/workflows/update_renv_push.yml

@@ -0,0 +1,30 @@
+name: Update renv Branch
+
+on:
+  push:
+    branches: [main]
+
+permissions: write-all
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Git User
+        run: |
+          git config user.name "GitHub Action"
+          git config user.email "<EMAIL>"
+
+      - name: Update Test Branch
+        run: |
+          git checkout main
+          git fetch origin
+          git checkout renv
+          git pull
+          git merge origin/main
+          git push origin renv

.gitignore

@@ -2,3 +2,7 @@
 .Rhistory
 .RData
 .Ruserdata
+.ipynb_checkpoints/
+.DS_Store
+
+/.quarto/

README.md

@@ -1,56 +1,48 @@
-# Reproducible Publications with Rstudio (Project Example)
+# Project Example for: Introduction to Reproducible Publications with Quarto Workshop
 
-Attention: This is NOT the lesson repository. This is the GitHub repository for the project example used in the [Introduction to Reproducible Publications with Rstudio Workshop](https://github.com/carpentries-incubator/Reproducible-Publications-with-RStudio). Learners will be required to download the project example in order to follow along. 
-Our example uses an adapted version of the data paper: Nitsch, F. J., Sellitto, M., & Kalenscher, T. (2021). The effects of acute and chronic stress on choice consistency. Psychoneuroendocrinology, 131, 105289. https://doi.org/10.1016/j.psyneuen.2021.105289. The data paper along with its underlying data publicly available at: https://osf.io/6mvq7 were adapted and used for educational purposes with authors' permission.
+*Attention!* This is NOT the lesson repository. This is the GitHub repository for the project example used in the [Introduction to Reproducible Publications with Quarto](https://github.com/UCSBCarpentry/Reproducible-Publications-with-RStudio-Quarto) **FIXME: UPDATE LINK WHEN PR TO INCUBATOR IS COMPLETED"**. Learners will be required to download the project example in order to follow along. 
+
+**The project example folder is a simplified version of the original project available at: https://osf.io/6mvq7.**
+
+Our example uses an adapted version of the data paper: Nitsch, F. J., Sellitto, M., & Kalenscher, T. (2021). The effects of acute and chronic stress on choice consistency. Psychoneuroendocrinology, 131, 105289. https://doi.org/10.1016/j.psyneuen.2021.105289. The data paper along with its underlying data publicly available at: https://osf.io/6mvq7 were adapted and used for educational purposes with the authors' permission.
 
 ------------------------------
-## README May 19 2022
-
-This directory contains the data and analysis scripts required
-to computationally reproduce the results and plots reported
-in "Nitsch, Sellitto & Kalenscher (2021). The effects
-of acute and chronic stress on choice consistency." Psychoneuroendocrinology.
-
-All provided code is written R (R version 4.0.0 (2020-04-24) -- "Arbor Day).
-It requires the following packages to run analysis code:
-- tidyverse 1.3.0
-- stringi 1.4.6
-- BayesFactor 0.9.12-4.2.
-- patchwork 1.0.0
-
-And the additional packages to render the R Markdown (.rmd) paper:
-- bookdown
-- tidyverse
-- knitr
-- rticles
-- rprojroot
-
+## README
+
+This directory contains the data and analysis scripts required to computationally reproduce some of the results and plots reported
+in "Nitsch, Sellitto & Kalenscher (2021). The effects of acute and chronic stress on choice consistency." Psychoneuroendocrinology that are used in this workshop.
+
+All provided code is written in R (R version 4.0.0 (2020-04-24) -- "Arbor Day") and should work with more recent versions. 
+It requires the following packages to run the analysis code:
+- tidyverse - 1.3.2
+- stringi - 1.7.8
+- bayesFactor - 0.9.12-4.5
+- patchwork - 1.1.3
+- usethis - 2.2.2 
+
 The structure of the directory is:
 
 root:
-- RStudio Project File
-- code #Contains all runnable R script files
-- data #Contains raw data
-    - foodchoice_data #Contains raw data from food choice task
-- output #Contain all generated output
-    - data #Contains preprocessed data
-    - plots #Contains all plots
-- paper
-    - source   # R Markdown paper file  
-    - output   # paper outputs
-    - bin   #Contains additional code for proper paper formatting (csl)
-- README.md
-- NitschEtAl2021.Rproj # R project file
-- LICENSE.md
-- CITATION.md
+
+- `Reproducible-Publications-with-RStudio-Example.Rproj` # RStudio Project File
+- `code` #Contains all runnable R script files
+- `data` 
+    - `processed`  # Contains processed data
+    - `raw`      # Contains raw data
+        - `foodchoice_data`  # Contains raw data from food choice task
+- `output` # Contain all generated output
+- `report`
+    - `DataPaper-ReproducibilityWorkshop_files`   # Rendered files  
+    - `fig`   # paper figures
+- `LICENSE.md`
+- `CITATION.md`
+- `README.md`
+- `_quarto.yml`
 
 To repeat the analyses, 
 1. Open the RStudio Project file.
 2. Open and run analyses scripts (in order)
 
-Note: data/foodchoice_budgetlines.csv is not required to run
-analysis scripts but is for information only.
-
 Graphic output is saved to output/plots
 Data output is saved to output/data
 Analysis results are saved in environment / printed to console
@@ -65,3 +57,5 @@ Enjoy!
 
 PS: For questions please email ucsbcarpentry (@) ucsb.edu.
 
+
+The `renv` branch has the same content as the `main` branch with the addition of having [renv](https://rstudio.github.io/renv/articles/renv.html) enabled for better reproducibility.

_quarto.yml

@@ -0,0 +1,5 @@
+project: 
+  title: "my-R-project.Rproj"
+
+editor: visual
+