rcompendium
:package: Create a package or compendium structure
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
○Committers with academic emails
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (19.6%) to scientific vocabulary
Keywords
package
r
reproducible-research
research-compendium
Last synced: 6 months ago
·
JSON representation
·
Repository
:package: Create a package or compendium structure
Basic Info
- Host: GitHub
- Owner: FRBCesab
- License: gpl-2.0
- Language: R
- Default Branch: main
- Homepage: https://frbcesab.github.io/rcompendium
- Size: 7.24 MB
Statistics
- Stars: 39
- Watchers: 1
- Forks: 9
- Open Issues: 4
- Releases: 6
Topics
package
r
reproducible-research
research-compendium
Created about 5 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Contributing
License
Code of conduct
Citation
Codemeta
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
rcompendium 
=========================================================
[](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/)
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. (2025) rcompendium: An R package to create a package or research
compendium structure. Version 1.4, 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 = {2025},
## note = {R package version 1.4},
## 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.
Owner
- Name: FRB CESAB
- Login: FRBCesab
- Kind: organization
- Location: Montpellier, FRANCE
- Website: https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/
- Repositories: 17
- Profile: https://github.com/FRBCesab
Citation (CITATION.cff)
# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
cff-version: 1.2.0
message: 'To cite package "rcompendium" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'rcompendium: Create a Package or Research Compendium Structure'
version: '1.4'
identifiers:
- type: doi
value: 10.32614/CRAN.package.rcompendium
abstract: 'Makes easier the creation of R package or 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 is set up with some
additional features: version control, remote repository creation, CI/CD configuration
(check package integrity under several OS, test code with ''testthat'', and build
and deploy website using ''pkgdown''). This package heavily relies on the R packages
''devtools'' and ''usethis'' and follows recommendations made by Wickham H. (2015)
<ISBN:9781491910597> and Marwick B. et al. (2018) <https://doi.org/10.7287/peerj.preprints.3192v2>.'
authors:
- family-names: Casajus
given-names: Nicolas
email: nicolas.casajus@fondationbiodiversite.fr
orcid: https://orcid.org/0000-0002-5537-5294
preferred-citation:
type: manual
title: 'rcompendium: An R package to create a package or research compendium structure'
authors:
- name: Casajus N.
year: '2025'
notes: R package version 1.4
url: https://github.com/FRBCesab/rcompendium
repository: https://CRAN.R-project.org/package=rcompendium
repository-code: https://github.com/FRBCesab/rcompendium
url: https://frbcesab.github.io/rcompendium/
contact:
- family-names: Casajus
given-names: Nicolas
email: nicolas.casajus@fondationbiodiversite.fr
orcid: https://orcid.org/0000-0002-5537-5294
keywords:
- package
- r
- reproducible-research
- research-compendium
references:
- type: software
title: 'R: A Language and Environment for Statistical Computing'
notes: Depends
url: https://www.R-project.org/
authors:
- name: R Core Team
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2025'
version: '>= 2.10'
- type: software
title: cffr
abstract: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages'
notes: Imports
url: https://docs.ropensci.org/cffr/
repository: https://CRAN.R-project.org/package=cffr
authors:
- family-names: Hernangómez
given-names: Diego
email: diego.hernangomezherrero@gmail.com
orcid: https://orcid.org/0000-0001-8457-4658
year: '2025'
doi: 10.32614/CRAN.package.cffr
- type: software
title: cli
abstract: 'cli: Helpers for Developing Command Line Interfaces'
notes: Imports
url: https://cli.r-lib.org
repository: https://CRAN.R-project.org/package=cli
authors:
- family-names: Csárdi
given-names: Gábor
email: gabor@posit.co
year: '2025'
doi: 10.32614/CRAN.package.cli
- type: software
title: codemetar
abstract: 'codemetar: Generate ''CodeMeta'' Metadata for R Packages'
notes: Imports
url: https://docs.ropensci.org/codemetar/
repository: https://CRAN.R-project.org/package=codemetar
authors:
- family-names: Boettiger
given-names: Carl
email: cboettig@gmail.com
orcid: https://orcid.org/0000-0002-1642-628X
- family-names: Salmon
given-names: Maëlle
orcid: https://orcid.org/0000-0002-2815-0399
year: '2025'
doi: 10.32614/CRAN.package.codemetar
- type: software
title: devtools
abstract: 'devtools: Tools to Make Developing R Packages Easier'
notes: Imports
url: https://devtools.r-lib.org/
repository: https://CRAN.R-project.org/package=devtools
authors:
- family-names: Wickham
given-names: Hadley
- family-names: Hester
given-names: Jim
- family-names: Chang
given-names: Winston
- family-names: Bryan
given-names: Jennifer
email: jenny@rstudio.com
orcid: https://orcid.org/0000-0002-6983-2759
year: '2025'
doi: 10.32614/CRAN.package.devtools
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title: gert
abstract: 'gert: Simple Git Client for R'
notes: Imports
url: https://docs.ropensci.org/gert/
repository: https://CRAN.R-project.org/package=gert
authors:
- family-names: Ooms
given-names: Jeroen
email: jeroenooms@gmail.com
orcid: https://orcid.org/0000-0002-4035-0289
year: '2025'
doi: 10.32614/CRAN.package.gert
- type: software
title: gh
abstract: 'gh: ''GitHub'' ''API'''
notes: Imports
url: https://gh.r-lib.org/
repository: https://CRAN.R-project.org/package=gh
authors:
- family-names: Bryan
given-names: Jennifer
- family-names: Wickham
given-names: Hadley
year: '2025'
doi: 10.32614/CRAN.package.gh
- type: software
title: gtools
abstract: 'gtools: Various R Programming Tools'
notes: Imports
url: https://github.com/r-gregmisc/gtools
repository: https://CRAN.R-project.org/package=gtools
authors:
- family-names: Warnes
given-names: Gregory R.
- family-names: Bolker
given-names: Ben
email: bolker@mcmaster.ca
orcid: https://orcid.org/0000-0002-2127-0443
- family-names: Lumley
given-names: Thomas
- family-names: Magnusson
given-names: Arni
- family-names: Venables
given-names: Bill
- family-names: Ryodan
given-names: Genei
- family-names: Moeller
given-names: Steffen
year: '2025'
doi: 10.32614/CRAN.package.gtools
- type: software
title: renv
abstract: 'renv: Project Environments'
notes: Imports
url: https://rstudio.github.io/renv/
repository: https://CRAN.R-project.org/package=renv
authors:
- family-names: Ushey
given-names: Kevin
email: kevin@rstudio.com
orcid: https://orcid.org/0000-0003-2880-7407
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
orcid: https://orcid.org/0000-0003-4757-117X
year: '2025'
doi: 10.32614/CRAN.package.renv
- type: software
title: rmarkdown
abstract: 'rmarkdown: Dynamic Documents for R'
notes: Imports
url: https://pkgs.rstudio.com/rmarkdown/
repository: https://CRAN.R-project.org/package=rmarkdown
authors:
- family-names: Allaire
given-names: JJ
email: jj@posit.co
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
- family-names: Dervieux
given-names: Christophe
email: cderv@posit.co
orcid: https://orcid.org/0000-0003-4474-2498
- family-names: McPherson
given-names: Jonathan
email: jonathan@posit.co
- family-names: Luraschi
given-names: Javier
- family-names: Ushey
given-names: Kevin
email: kevin@posit.co
- family-names: Atkins
given-names: Aron
email: aron@posit.co
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Chang
given-names: Winston
email: winston@posit.co
- family-names: Iannone
given-names: Richard
email: rich@posit.co
orcid: https://orcid.org/0000-0003-3925-190X
year: '2025'
doi: 10.32614/CRAN.package.rmarkdown
- type: software
title: rstudioapi
abstract: 'rstudioapi: Safely Access the RStudio API'
notes: Imports
url: https://rstudio.github.io/rstudioapi/
repository: https://CRAN.R-project.org/package=rstudioapi
authors:
- family-names: Ushey
given-names: Kevin
email: kevin@rstudio.com
- family-names: Allaire
given-names: JJ
email: jj@posit.co
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Ritchie
given-names: Gary
email: gary@posit.co
year: '2025'
doi: 10.32614/CRAN.package.rstudioapi
- type: software
title: stringr
abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
notes: Imports
url: https://stringr.tidyverse.org
repository: https://CRAN.R-project.org/package=stringr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2025'
doi: 10.32614/CRAN.package.stringr
- type: software
title: usethis
abstract: 'usethis: Automate Package and Project Setup'
notes: Imports
url: https://usethis.r-lib.org
repository: https://CRAN.R-project.org/package=usethis
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
orcid: https://orcid.org/0000-0003-4757-117X
- family-names: Bryan
given-names: Jennifer
email: jenny@posit.co
orcid: https://orcid.org/0000-0002-6983-2759
- family-names: Barrett
given-names: Malcolm
email: malcolmbarrett@gmail.com
orcid: https://orcid.org/0000-0003-0299-5825
- family-names: Teucher
given-names: Andy
email: andy.teucher@posit.co
orcid: https://orcid.org/0000-0002-7840-692X
year: '2025'
doi: 10.32614/CRAN.package.usethis
- type: software
title: utils
abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
- name: R Core Team
institution:
name: R Foundation for Statistical Computing
address: Vienna, Austria
year: '2025'
- type: software
title: xfun
abstract: 'xfun: Supporting Functions for Packages Maintained by ''Yihui Xie'''
notes: Imports
url: https://github.com/yihui/xfun
repository: https://CRAN.R-project.org/package=xfun
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2025'
doi: 10.32614/CRAN.package.xfun
- type: software
title: fs
abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
notes: Suggests
url: https://fs.r-lib.org
repository: https://CRAN.R-project.org/package=fs
authors:
- family-names: Hester
given-names: Jim
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Csárdi
given-names: Gábor
email: csardi.gabor@gmail.com
year: '2025'
doi: 10.32614/CRAN.package.fs
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
notes: Suggests
url: https://yihui.org/knitr/
repository: https://CRAN.R-project.org/package=knitr
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2025'
doi: 10.32614/CRAN.package.knitr
- type: software
title: testthat
abstract: 'testthat: Unit Testing for R'
notes: Suggests
url: https://testthat.r-lib.org
repository: https://CRAN.R-project.org/package=testthat
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2025'
doi: 10.32614/CRAN.package.testthat
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notes: Suggests
url: https://withr.r-lib.org
repository: https://CRAN.R-project.org/package=withr
authors:
- family-names: Hester
given-names: Jim
- family-names: Henry
given-names: Lionel
email: lionel@posit.co
- family-names: Müller
given-names: Kirill
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- family-names: Ushey
given-names: Kevin
email: kevinushey@gmail.com
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Chang
given-names: Winston
year: '2025'
doi: 10.32614/CRAN.package.withr
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],
"keywords": [
"r",
"package",
"research-compendium",
"reproducible-research"
]
}GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 6
- Watch event: 2
- Issue comment event: 5
- Push event: 22
- Pull request event: 1
- Fork event: 1
Last Year
- Create event: 1
- Release event: 1
- Issues event: 6
- Watch event: 2
- Issue comment event: 5
- Push event: 22
- Pull request event: 1
- Fork event: 1
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Nicolas Casajus | n****s@g****m | 250 |
| olivroy | 5****y | 5 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 67
- Total pull requests: 6
- Average time to close issues: 27 days
- Average time to close pull requests: about 2 months
- Total issue authors: 8
- Total pull request authors: 2
- Average comments per issue: 0.46
- Average comments per pull request: 0.83
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 0
- Average time to close issues: 2 months
- Average time to close pull requests: N/A
- Issue authors: 3
- Pull request authors: 0
- Average comments per issue: 0.25
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ahasverus (59)
- Pakillo (2)
- morfogeno (1)
- avallecam (1)
- LPDagallier (1)
- woncoh1 (1)
- see24 (1)
- olivroy (1)
Pull Request Authors
- olivroy (4)
- see24 (2)
Top Labels
Issue Labels
enhancement (28)
bug (12)
documentation (4)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 792 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 5
- Total maintainers: 1
cran.r-project.org: rcompendium
Create a Package or Research Compendium Structure
- Homepage: https://github.com/FRBCesab/rcompendium
- Documentation: http://cran.r-project.org/web/packages/rcompendium/rcompendium.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
-
Latest release: 0.5.1
published almost 5 years ago
Rankings
Stargazers count: 9.0%
Forks count: 9.6%
Average: 18.0%
Downloads: 18.8%
Dependent repos count: 23.8%
Dependent packages count: 28.6%
Maintainers (1)
Last synced:
6 months ago
Dependencies
DESCRIPTION
cran
- R >= 2.10 depends
- clisymbols * imports
- crayon * imports
- devtools * imports
- gert * imports
- gh * imports
- gtools * imports
- renv * imports
- rmarkdown * imports
- rstudioapi * imports
- stringr * imports
- usethis * imports
- utils * imports
- xfun * imports
- fs * suggests
- knitr * suggests
- testthat >= 3.0.0 suggests
- withr * suggests
.github/workflows/R-CMD-check.yaml
actions
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/document-package.yaml
actions
- actions/checkout v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml
actions
- JamesIves/github-pages-deploy-action v4.4.1 composite
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/render-README.yaml
actions
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
.github/workflows/test-coverage.yaml
actions
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/update-citation-cff.yaml
actions
- actions/checkout v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
inst/templates/DESCRIPTION
cran
inst/templates/Dockerfile
docker
- rocker/rstudio {{r_version}} build