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README.Rmd
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README.Rmd
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---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
rcompendium <img src="man/figures/logo.png" align="right" style="float:right; height:120px;"/>
=========================================================
<!-- badges: start -->
[](https://CRAN.R-project.org/package=rcompendium/)
[](https://github.com/FRBCesab/rcompendium/actions/workflows/R-CMD-check.yaml)
[](https://github.com/FRBCesab/rcompendium/actions/workflows/pkgdown.yaml)
[](https://app.codecov.io/gh/FRBCesab/rcompendium)
[](https://choosealicense.com/licenses/gpl-2.0/)
<!-- badges: end -->
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 version control with [git](https://git-scm.com/).
- 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/` (package only).
- Setting the units tests process in `tests/`.
- Creation of a `README.Rmd` with HexSticker (template) and badges.
- Autocompletion of maintainer information.
- Initialization of the `renv` system (if required).
- Creation of a Dockerfile (if required).
- 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`);
- render `README.md`.
This package heavily relies on the R packages
[`devtools`](https://devtools.r-lib.org) and
[`usethis`](https://usethis.r-lib.org) and follows recommendations made by
[Hadley Wickham & Jenny Bryan](https://r-pkgs.org) and
[Ben Marwick](https://peerj.com/preprints/3192/).
## Installation
You can install the stable version from [CRAN](https://cran.r-project.org/) with:
```{r eval=FALSE}
## Install stable version of < rcompendium > from CRAN ----
install.packages("rcompendium")
```
Or you can install the development version from [GitHub](https://github.com/) with:
```{r eval=FALSE}
## 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")
```
**Note:** On Unix system you may have an error during the installation linked
to the [**V8 JavaScript engine**](https://v8.dev/). This software is required
by the R package [`cffr`](https://docs.ropensci.org/cffr/)
(included in `rcompendium`). Run the following line and try to reinstall `rcompendium`.
```{r eval=FALSE}
## Fix V8 issues ----
Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1)
## Install < rcompendium > ----
install.packages("rcompendium")
```
## Usage
Please read the
[Get started](https://frbcesab.github.io/rcompendium/articles/rcompendium.html) vignette
and pay attention to the sections
[Prerequisites](https://frbcesab.github.io/rcompendium/articles/rcompendium.html#prerequisites) and
[Usage](https://frbcesab.github.io/rcompendium/articles/rcompendium.html#usage)
Others available vignettes:
- [Developing a Package](https://frbcesab.github.io/rcompendium/articles/developing_a_package.html)
- [Working with a Compendium](https://frbcesab.github.io/rcompendium/articles/working_with_a_compendium.html)
## Citation
Please cite this package as:
> Casajus N. (2023) rcompendium: An R package to create a package or research
compendium structure. Version 1.3, https://github.com/FRBCesab/rcompendium.
You can also run:
```{r eval=FALSE}
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 = {2023},
## note = {R package version 1.3},
## url = {https://github.com/FRBCesab/rcompendium},
## }
```
## Contributing
All types of contributions are encouraged and valued. For more information,
check out our [Contribution Guidelines](https://github.com/FRBCesab/rcompendium/blob/main/CONTRIBUTING.md).
Please note that the `rcompendium` project is released with a
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.
## Colophon
This package is the result of intense discussions and feedbacks from the training
course [Reproducible Research in Computational Ecology](https://rdatatoolbox.github.io/).
`rcompendium` is largely inspired by the package
[`rrtools`](https://github.com/benmarwick/rrtools) developed by
[Ben Marwick _et al._](https://github.com/benmarwick) and tries to respect the standard
defined by the community.