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https://github.com/carpentries-incubator/quarto-project-example

Project Example for the Lesson: Introduction to Reproducible Publications with Quarto
https://github.com/carpentries-incubator/quarto-project-example

alpha carpentries-incubator english open-science project-management qmd quarto r reproducible-paper rstudio scientific-reproducibility

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Project Example for the Lesson: Introduction to Reproducible Publications with Quarto

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README 

        
# Project Example for the Workshop: 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](https://github.com/carpentries-incubator/reproducible-publications-quarto). 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](https://osf.io/6mvq7).**



Our example uses an adapted version of the data paper: 



Nitsch, F. J., Sellitto, M., & Kalenscher, T. (2021). Trier social stress test and food-choice: Behavioral, self-report & hormonal data. *Data in Brief*, 37, 107245. [https://doi.org/10.1016/j.dib.2021.107245](https://doi.org/10.1016/j.dib.2021.107245).



The data paper and its underlying data publicly available at [https://osf.io/6mvq7](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 [https://doi.org/10.1016/j.dib.2021.107245](https://doi.org/10.1016/j.dib.2021.107245).



All provided code was 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 analysis scripts (in order)



Graphic output is saved to output/plots

Data output is saved to output/data

Analysis results are saved in the environment / printed to the 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. 



**Note:** 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.



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.



Contributors:



* Renata Curty (rcurty)

* Torin White (torwhite)

* Ian Lessing (ilessing)

* Greg Janee (gjanee)

* Julien Brun (brunj7)

* kristi Liu (kristi-sara)