Reproducible Publications with Rstudio (Project Example)

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. 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 the authors' permission.

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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

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

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 Paper output is saved to paper/output paper/bin contains external files/code necessary for the proper formatting of the R Markdown paper output.

Please see citation.md for instructions on how to cite this workshop.

Please see License.md for instructions on how to re-use this material.

Enjoy!

PS: For questions please email ucsbcarpentry (@) ucsb.edu.