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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 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

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:

  • 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)

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.

The renv branch has the same content as the main branch with the addition of having renv enabled for better reproducibility.