rcompendium

In the area of open science, making reproducible analyses is a strong prerequisite. But sometimes it is difficult 1) to find the good structure to organize files and 2) to set up the whole project. The aim of the package rcompendium is to make easier the creation of R package/research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files.

A full ready-to-work structure will be set up with the following features:

• Initialization of the GIT version control.
• Creation of a minimal R package structure (DESCRIPTION and NAMESPACE files, and R/ and man/ folders).
• Creation of additional files (LICENSE.md, inst/CITATION, etc.).
• Creation of a Get started vignette in vignettes/.
• Setting the units tests process.
• Creation of a README.Rmd with HexSticker (template) and badges.
• Autocompletion of maintainer information.
• Creation of a GitHub repository.
• Configuration of GitHub Actions to automatically:
  • check and test package (R CMD Check);
  • report the code coverage (covr);
  • build and deploy website (pkgdown).

This package heavily relies on the R packages devtools and usethis and follows recommendations made by Hadley Wickham & Jenny Bryan and Ben Marwick.

Overview

The strength of rcompendium is to create the whole structure in one command line by using the function new_package() (or new_compendium()). The default settings will produce the following structure:

.
│
├── pkg.Rproj                   # (optional) Created by user 
│
├── .git/                       # GIT tracking folder
├── .gitignore                  # Specific to R packages
|
├── .github/                    # (optional) GitHub Actions settings
│   └── workflows/
│       ├── pkgdown.yaml        # Configuration file to build & deploy website
│       ├── R-CMD-check.yaml    # Configuration file to check & test package
│       └── test-coverage.yaml  # Configuration file to build & deploy website
│
├── _pkgdown.yaml               # (optional) User website settings
│
├── R/                          # R functions
│   ├── fun-demo.R              # Example of an R function
│   └── pkg-package.R           # Dummy R file for package-level documentation
│
├── man/                        # R functions helps (automatically updated)
│   ├── print_msg.Rd            # Documentation of the demo R function
│   ├── pkg-package.Rd          # Package-level documentation
│   └── figures/                # Figures for the README 
│       └── hexsticker.png      # Template R package HexSticker
│
├── tests/
│   ├── testthat.R              # Units tests settings
│   └── testthat/               # Units tests folder
│       └── test-demo.R         # Units tests for the function print_msg()
|
├── vignettes/
│   └── pkg.Rmd                 # (optional) Package tutorial              [*]
│
├── DESCRIPTION                 # Project metadata                         [*]
├── NAMESPACE                   # Automatically generated
├── .Rbuildignore               # List of files/folders to be ignored while 
│                               # checking the package
├── inst/
│   └── CITATION                # BiBTeX entry to cite the R package       [*]
│
├── LICENSE                     # (optional) If License = MIT
├── LICENSE.md                  # Content of the chosen license
│
├── README.md                   # GitHub README (automatically generated)
├── README.Rmd                  # GitHub README (to knit)                  [*]
/
/
├── data/                       # User raw data (.csv, .gpkg, etc.)        [¶]
├── analyses/                   # R scripts (no functions) to run analyses [¶]
├── outputs/                    # Outputs created by R scripts             [¶]
└── figures/                    # Figures created by R scripts             [¶]
│
└── make.R                      # Master R scripts to run all analyses     [¶]


[*] These files are automatically edited but user needs to add manually 
    some information.
[¶] These folders/files are also created when using new_compendium().

Installation

You can install the stable version from CRAN with:

## Install stable version of < rcompendium > from CRAN ----
install.packages("rcompendium")

Or you can install the development version from GitHub with:

## Install < remotes > package (if not already installed) ----
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

## Install dev version of < rcompendium > from GitHub ----
remotes::install_github("FRBCesab/rcompendium")

Get started

Please read the Vignette and pay attention to the sections Prerequisites and Usage

💥 This package was created by running:

rcompendium::new_package()

💥 This research compendium was created by running:

rcompendium::new_compendium()

N.B. Before running these commands, a new RStudio project needs to be created.

Citation

Please cite this package as:

Casajus N. (2021) rcompendium: An R package to create a package or research compendium structure. Version 0.5.1, https://github.com/FRBCesab/rcompendium.

You can also run:

citation("rcompendium")

## A BibTeX entry for LaTeX users is:
## 
## @Manual{,
##   title  = {{rcompendium}: {An} {R} package to create a package or research compendium structure},
##   author = {{Casajus N.}},
##   year   = {2021},
##   note   = {R package version 0.5.1},
##   url    = {https://github.com/FRBCesab/rcompendium},
## }

Contributing

You are welcome to contribute to the rcompendium project. Please read our Contribution Guidelines.

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

Colophon

This package is the result of intense discussions and feedback from the training course Data Toolbox for Reproducible Research in Computational Ecology (in French).

rcompendium is largely inspired by the package rrtools developed by Ben Marwick et al. and tries to respect the standard defined by the community. Special thanks to these developers!