Science Score: 67.0%
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
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (19.8%) to scientific vocabulary
Keywords
r
r-package
Last synced: 6 months ago
·
JSON representation
·
Repository
Basic Info
- Host: GitHub
- Owner: b-cubed-eu
- License: other
- Language: R
- Default Branch: main
- Homepage: https://b-cubed-eu.github.io/b3doc/
- Size: 1.14 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 2
- Releases: 2
Topics
r
r-package
Created about 1 year ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Contributing
License
Code of conduct
Citation
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# b3doc
[](https://www.repostatus.org/#active)
[](https://github.com/b-cubed-eu/b3doc/releases)
[](https://b-cubed-eu.r-universe.dev/b3doc)
[](https://CRAN.R-project.org/package=b3doc)
[](https://github.com/b-cubed-eu/b3doc/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/b-cubed-eu/b3doc)
[](https://doi.org/10.5281/zenodo.15649519)
[](https://b-cubed-eu.r-universe.dev/)
b3doc is an R package to create Markdown pages for the [B-Cubed documentation website](https://docs.b-cubed.eu) from external R Markdown files, such as vignettes. The package has functionality to set the necessary metadata in the front matter.
To get started, see:
- [Function reference](https://b-cubed-eu.github.io/b3doc/reference/index.html): overview of all functions.
## Installation
You can install the development version of b3doc from [GitHub](https://github.com/b-cubed-eu/b3doc) with:
``` r
# install.packages("remotes")
remotes::install_github("b-cubed-eu/b3doc")
```
## Usage
Here we use b3doc to read a [vignette](https://github.com/b-cubed-eu/gcube/blob/main/vignettes/articles/occurrence-process.Rmd), run its code and output a Markdown file:
``` r
library(b3doc)
# Load packages used in the Rmd file
library(sf)
library(dplyr)
library(ggplot2)
library(tidyterra)
# Convert Rmd to Markdown
rmd_to_md(
rmd_file = "https://raw.githubusercontent.com/b-cubed-eu/gcube/refs/heads/main/vignettes/articles/occurrence-process.Rmd",
md_dir = "output/src/content/docs/software/gcube",
fig_dir = "output/public/software/gcube",
fig_url_dir = "/software/gcube/",
title = "2. Occurrence process",
sidebar_label = "occurrence-process",
sidebar_order = 2
)
# Clean up (don't do this if you want to keep your files)
unlink("output", recursive = TRUE)
```
In production, this code is run as part of a [script](https://github.com/b-cubed-eu/documentation/blob/main/src/rmd_to_md/rmd_to_md.Rmd) to update the [B-Cubed documentation website](https://docs.b-cubed.eu). Its static website generator then builds the site, using the metadata we provided (such as `sidebar_label`).
## Meta
- We welcome [contributions](https://b-cubed-eu.github.io/b3doc/CONTRIBUTING.html) including bug reports.
- License: MIT
- Get [citation information](https://b-cubed-eu.github.io/b3doc/authors.html#citation) for b3doc in R doing `citation("b3doc")`.
- Please note that this project is released with a [Contributor Code of Conduct](https://b-cubed-eu.github.io/b3doc/CODE_OF_CONDUCT.html). By participating in this project you agree to abide by its terms.
## Acknowledgments
This software was developed with funding from the European Union's Horizon Europe Research and Innovation Programme under grant agreement ID No [101059592](https://doi.org/10.3030/101059592).
Owner
- Name: B-Cubed
- Login: b-cubed-eu
- Kind: organization
- Website: https://b-cubed.eu
- Repositories: 1
- Profile: https://github.com/b-cubed-eu
Biodiversity Building Blocks for Policy
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 "b3doc" in publications use:'
type: software
license: MIT
title: 'b3doc: Tools for the B-Cubed Documentation Website'
version: 0.2.0
abstract: Create Markdown pages for the B-Cubed documentation website (<https://docs.b-cubed.eu>)
from external R Markdown files, such as vignettes.
authors:
- family-names: Govaert
given-names: Sanne
email: sanne.govaert@inbo.be
orcid: https://orcid.org/0000-0002-8939-1305
affiliation: Research Institute for Nature and Forest (INBO)
- family-names: Desmet
given-names: Peter
email: peter.desmet@inbo.be
orcid: https://orcid.org/0000-0002-8442-8025
affiliation: Research Institute for Nature and Forest (INBO)
- family-names: Huybrechts
given-names: Pieter
email: pieter.huybrechts@inbo.be
orcid: https://orcid.org/0000-0002-6658-6062
affiliation: Research Institute for Nature and Forest (INBO)
- family-names: Langeraert
given-names: Ward
email: ward.langeraert@inbo.be
orcid: https://orcid.org/0000-0002-5900-8109
affiliation: Research Institute for Nature and Forest (INBO)
repository-code: https://github.com/b-cubed-eu/b3doc
url: https://b-cubed-eu.github.io/b3doc/
date-released: '2025-08-20'
contact:
- family-names: Govaert
given-names: Sanne
email: sanne.govaert@inbo.be
orcid: https://orcid.org/0000-0002-8939-1305
affiliation: Research Institute for Nature and Forest (INBO)
keywords:
- r
- r-package
references:
- 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: fs
abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
notes: Imports
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: Imports
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: R.utils
abstract: 'R.utils: Various Programming Utilities'
notes: Imports
url: https://henrikbengtsson.github.io/R.utils/
repository: https://CRAN.R-project.org/package=R.utils
authors:
- family-names: Bengtsson
given-names: Henrik
email: henrikb@braju.com
year: '2025'
doi: 10.32614/CRAN.package.R.utils
- 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: 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: yaml
abstract: 'yaml: Methods to Convert R Data to YAML and Back'
notes: Imports
url: https://github.com/vubiostat/r-yaml/
repository: https://CRAN.R-project.org/package=yaml
authors:
- family-names: Garbett
given-names: Shawn P
- family-names: Stephens
given-names: Jeremy
- family-names: Simonov
given-names: Kirill
- family-names: Xie
given-names: Yihui
- family-names: Dong
given-names: Zhuoer
- family-names: Wickham
given-names: Hadley
- family-names: Horner
given-names: Jeffrey
- name: reikoch
- family-names: Beasley
given-names: Will
- family-names: O'Connor
given-names: Brendan
- family-names: Warnes
given-names: Gregory R.
- family-names: Quinn
given-names: Michael
- family-names: Kamvar
given-names: Zhian N.
- family-names: Gao
given-names: Charlie
year: '2025'
doi: 10.32614/CRAN.package.yaml
- type: software
title: curl
abstract: 'curl: A Modern and Flexible Web Client for R'
notes: Suggests
url: https://jeroen.r-universe.dev/curl
repository: https://CRAN.R-project.org/package=curl
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.curl
- type: software
title: here
abstract: 'here: A Simpler Way to Find Your Files'
notes: Suggests
url: https://here.r-lib.org/
repository: https://CRAN.R-project.org/package=here
authors:
- family-names: Müller
given-names: Kirill
email: krlmlr+r@mailbox.org
orcid: https://orcid.org/0000-0002-1416-3412
year: '2025'
doi: 10.32614/CRAN.package.here
- type: software
title: rmarkdown
abstract: 'rmarkdown: Dynamic Documents for R'
notes: Suggests
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: 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
version: '>= 3.0.0'
GitHub Events
Total
- Create event: 14
- Commit comment event: 1
- Release event: 4
- Issues event: 15
- Delete event: 10
- Issue comment event: 39
- Member event: 4
- Push event: 102
- Pull request review event: 15
- Pull request event: 14
- Pull request review comment event: 13
Last Year
- Create event: 14
- Commit comment event: 1
- Release event: 4
- Issues event: 15
- Delete event: 10
- Issue comment event: 39
- Member event: 4
- Push event: 102
- Pull request review event: 15
- Pull request event: 14
- Pull request review comment event: 13
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- PietrH (4)
- peterdesmet (2)
- sannegovaert (2)
- wlangera (1)
Pull Request Authors
- sannegovaert (5)
- peterdesmet (2)
- PietrH (1)
Top Labels
Issue Labels
documentation (2)
Pull Request Labels
Dependencies
.github/workflows/R-CMD-check.yaml
actions
- actions/checkout v4 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/test-coverage.yaml
actions
- actions/checkout v4 composite
- actions/upload-artifact v4 composite
- codecov/codecov-action v4 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION
cran