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https://github.com/FRBCesab/rcompendium

:package: Create a package or compendium structure
https://github.com/FRBCesab/rcompendium

package r reproducible-research research-compendium

Last synced: about 1 month ago
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:package: Create a package or compendium structure

Lists

README 

        
---

output: github_document

---



```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse  = TRUE,

  comment   = "#>",

  fig.path  = "man/figures/README-",

  out.width = "100%"

)

```



rcompendium 

=========================================================



[![CRAN status](https://www.r-pkg.org/badges/version/rcompendium)](https://CRAN.R-project.org/package=rcompendium/)

[![R CMD check](https://github.com/FRBCesab/rcompendium/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FRBCesab/rcompendium/actions/workflows/R-CMD-check.yaml)

[![Website deployment](https://github.com/FRBCesab/rcompendium/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/FRBCesab/rcompendium/actions/workflows/pkgdown.yaml)

[![codecov](https://codecov.io/gh/FRBCesab/rcompendium/branch/main/graph/badge.svg)](https://app.codecov.io/gh/FRBCesab/rcompendium)

[![License: GPL (>= 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)



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.