Code Management Guidelines: R and GitHub Starter Kit for New Team Members

Description

This book aims to provide a basic usage guide for new lab members regarding the handling of data and code with R and GitHub platform.

It provides:

• A series of steps for onboarding.

• Instructions on programs to install.

• A guide to starting a project.

• Recommendations on best practices.

• Instructions on how to push locally created code to GitHub using RStudio.

Installation and Setup

Follow these steps only in case you want to edit the book:

1. Clone the repository:

git clone [email protected]:StringhiniLab/GitHubProceduresLab.git

2. Install dependencies using renv:

install.packages("renv")
renv::restore()

3. Open the project in RStudio and compile the book running:

quarto render

Contact

If you have any questions or suggestions, please contact open a GitHub issue.

Code of Conduct

Please note that the github_procedures project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Cite Us

If you use this manual, please cite it as follows:

D'Andrea, F., & Stringhini, S. Code Management Guidelines: R and GitHub Starter Kit for New Team Members. https://github.com/StringhiniLab/GitHubProceduresLab. https://doi.org/10.5281/zenodo.14510774

Session Info

The current environment setup is managed using renv to ensure reproducibility. The session info is as follows:

R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.5

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] usethis_3.1.0

loaded via a namespace (and not attached):
 [1] fansi_1.0.6       withr_3.0.2       rprojroot_2.0.4   utf8_1.2.4       
 [5] lifecycle_1.0.4   magrittr_2.0.3    pillar_1.9.0      rlang_1.1.4      
 [9] cli_3.6.3         renv_1.0.3        rstudioapi_0.17.1 fs_1.6.5         
[13] whisker_0.4.1     vctrs_0.6.5       tools_4.2.1       glue_1.8.0       
[17] purrr_1.0.2       compiler_4.2.1    pkgconfig_2.0.3   clipr_0.8.0      
[21] tibble_3.2.1