RStudio-reproducibility-example

This is the GitHub repository for the example used in the Reproducibility with R Markdown in RStudio workshop. 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.

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README 17 Nov 2021

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.