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.
Follow these steps only in case you want to edit the book:
- Clone the repository:
git clone git@github.com:StringhiniLab/GitHubProceduresLab.git- Install dependencies using
renv:
install.packages("renv") renv::restore()- Open the project in RStudio and compile the book running:
quarto renderIf you have any questions or suggestions, please contact open a GitHub issue.
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.
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
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