worcs

Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)

https://github.com/cjvanlissa/worcs

Science Score: 67.0%

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  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
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  • .zenodo.json file
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  • DOI references
    Found 1 DOI reference(s) in README
  • Academic publication links
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    2 of 13 committers (15.4%) from academic institutions
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    Low similarity (19.1%) to scientific vocabulary

Keywords from Contributors

http-mock structural-equation-modeling reproducibility
Last synced: 6 months ago · JSON representation ·

Repository

Rstudio project template and convenience functions for the Workflow for Open Reproducible Code in Science (WORCS)

Basic Info
Statistics
  • Stars: 84
  • Watchers: 7
  • Forks: 11
  • Open Issues: 38
  • Releases: 7
Created about 6 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation

README.Rmd

---
output: github_document
---

# WORCS worcs website




[![CRAN status](https://www.r-pkg.org/badges/version/worcs)](https://cran.r-project.org/package=worcs)
[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/worcs?color=blue)](https://r-pkg.org/pkg/worcs)
[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing)
[![R-CMD-check](https://github.com/cjvanlissa/worcs/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cjvanlissa/worcs/actions/workflows/R-CMD-check.yaml)
[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](code_of_conduct.md)
[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/3969/badge)](https://bestpractices.coreinfrastructure.org/projects/3969)


The Workflow for Open Reproducible Code in Science (WORCS) is an easy to adopt approach to ensuring a research project meets the requirements of Open Science from the start. It is based on a "good enough" philosophy, prioritizing user-friendliness over exhaustiveness. It can be used either in absence of, or in parallel to, existing requirements for Open workflows. It can also be enhanced with more elaborate solutions for specific issues.

## Where do I start?

For most users, the recommended starting point is to [read the paper, published in Data Science](https://content.iospress.com/articles/data-science/ds210031),
which introduces the WORCS workflow, explains the underlying tools, and illustrates how the `worcs` package can be used to create a new project that follows the workflow.

The workflow is illustrated below; the [workflow vignette](https://cjvanlissa.github.io/worcs/articles/workflow.html) describes each step in detail.

```{r, echo = FALSE, fig.alt="A diagram of the WORCS workflow."}
knitr::include_graphics("https://github.com/cjvanlissa/worcs/raw/master/paper/workflow_graph/workflow.png")
```


## Installing the package

Before installing the package, please read [this vignette](https://cjvanlissa.github.io/worcs/articles/setup.html), which explains how to set up your computer for `worcs` (using the CRAN version).

If you know what you're doing and you wish to install the development version of the `worcs` package from GitHub instead, you can use:

``` r
if(!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("cjvanlissa/worcs", dependencies = TRUE, update = "never")
```

## Citing WORCS

You can cite WORCS using the following citation (please use the same citation for either the package, or the paper):

> Van Lissa, C. J., Brandmaier, A. M., Brinkman, L., Lamprecht, A., Peikert, A., , Struiksma, M. E., & Vreede, B. (2021). WORCS: A Workflow for Open Reproducible Code in Science. Data Science. Data Science, vol. 4, no. 1, pp. 29-49. DOI: 10.3233/DS-210031.

## About this repository

This repository contains the following:

1.  An R-package called `worcs`, with convenience functions to facilitate the WORCS workflow.
2.  In the subfolder `./paper`, the source files for the paper describing the WORCS workflow.

The repository serves two functions: To allow users to install the `worcs` package, and to allow collaborators access to the source code for the package and paper.

## Repository structure

```{r echo = FALSE, results = "asis"}
descripts <- data.frame(matrix(c(
  "_pkgdown.yml", "YAML for package website", "do not edit",
  "DESCRIPTION", "R-package DESCRIPTION", "do not edit",
  "LICENSE.md", "Project license", "do not edit",
  "NAMESPACE", "R-package namespace", "machine-written",
  "README.md", "Read this file to get started! ", "do not edit",
  "README.Rmd", "R-markdown source for readme.md", "human editable",
  "worcs.Rproj", "RStudio project file", "do not edit",
  "docs/", "Package website", "machine-written",
  "inst/", "RStudio project template files ", "human editable",
  "man/", "R-package documentation", "do not edit",
  "paper/", "WORCS paper source files", "human editable",
  "R/", "R-package source code", "human editable",
  "vignettes/", "R-package vignettes", "human editable"
), ncol = 3, byrow = TRUE))
names(descripts) <- c("File", "Description", "Usage")
knitr::kable(descripts)
```



```{r, eval = FALSE, echo = FALSE, message=FALSE, warning=FALSE}
library(gh)
library(dlstats)
dl <- dlstats::cran_stats("worcs")
dl <- sum(dl$downloads)

# worcs_repo <- gh("/repos/cjvanlissa/worcs")
# 
# repos <- gh("GET /search/code", username = "cjvanlissa", q="worcs_version filename:.worcs")
# 
# worcs_repos <- data.frame(t(sapply(repos[["items"]], function(x){
#   c(owner = x$repository$owner$login,
#     name = x$repository$name,
#     url = x$repository$html_url
#   )
# })))

# worcs_repos <- worcs_repos[!((worcs_repos$owner %in% c("cjvanlissa", "cran") & worcs_repos$name == "worcs")| grepl("(penguin|\\btmp|demo|test)", tolower(worcs_repos$name))), ]

# tmp <- paste0(sapply(unique(worcs_repos$owner), function(x){
#   owner_repos <- worcs_repos[worcs_repos$owner == x, , drop = FALSE]
#   paste0("\n    - ", x, "  ",
#          paste0("\n        + [", owner_repos$name, "](", owner_repos$url, ")  ", collapse = ""))
#   }),
#   collapse = "")

# invited <- read.table("https://raw.githubusercontent.com/cjvanlissa/resume/master/invited.csv", sep = ",", header = TRUE)
# invited <- invited[grepl("(worcs|workflow)", tolower(invited$Topic)), c("Institute", "Year", "City", "Country", "Date")]
# invited <- paste0(apply(invited, 1, function(x){paste0("\n    - ", x[1], " (", x[2], ")  ")}), collapse = "")
```











## Contributing and Contact Information

We are always eager to receive user feedback and contributions to help us improve both the workflow and the software. Major contributions warrant coauthorship to the package. Please contact the lead author at [c.j.vanlissa@uu.nl](mailto:c.j.vanlissa@uu.nl), or:

  - [File a GitHub issue](https://github.com/cjvanlissa/worcs) for feedback, bug reports or feature requests
  - [Make a pull request](https://github.com/cjvanlissa/worcs/pulls) to contribute your code or prose

By participating in this project, you agree to abide by the [Contributor
Code of Conduct v2.0](https://www.contributor-covenant.org/). Contributions to the package must adhere to the [tidyverse style guide](https://style.tidyverse.org/). When contributing code, please add tests for that contribution to the `tests/testthat` folder, and ensure that these tests pass in the [GitHub Actions panel](https://github.com/cjvanlissa/worcs/actions/workflows/R-CMD-check).

## Acknowledgements

The worcs logo is inspired by the Open Science Badges by the Center for Open Science (CC-BY-4.0), and makes use of the gear, services, gears, preferences, settings icon, made by MD Badsha Meah from www.freeicons.io (CC-BY-3.0). 

Owner

  • Name: C. J. van Lissa
  • Login: cjvanlissa
  • Kind: user
  • Company: Utrecht University

Developmental datascientist, studying mothers' and fathers' unique roles in children's socio-emotional development.

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.2.2
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------

cff-version: 1.2.0
message: 'To cite package "worcs" in publications use:'
type: article
title: 'WORCS: A Workflow for Open Reproducible Code in Science'
authors:
- family-names: Van Lissa
  given-names: Caspar J.
- family-names: Brandmaier
  given-names: Andreas M.
- family-names: Brinkman
  given-names: Loek
- family-names: Lamprecht
  given-names: Anna-Lena
- family-names: Peikert
  given-names: Aaron
- family-names: Struiksma
  given-names: Marijn E.
- family-names: Vreede
  given-names: Barbara M.I.
year: '2021'
journal: Data Science
volume: '4'
issue: '1'
publisher:
  name: IOS Press
issn: 2451-8492
doi: 10.3233/DS-210031
abstract: 'Adopting open science principles can be challenging, requiring conceptual
  education and training in the use of new tools. This paper introduces the Workflow
  for Open Reproducible Code in Science (WORCS): A step-by-step procedure that researchers
  can follow to make a research project open and reproducible. This workflow intends
  to lower the threshold for adoption of open science principles. It is based on established
  best practices, and can be used either in parallel to, or in absence of, top-down
  requirements by journals, institutions, and funding bodies. To facilitate widespread
  adoption, the WORCS principles have been implemented in the R package worcs , which
  offers an RStudio project template and utility functions for specific workflow steps.
  This paper introduces the conceptual workflow, discusses how it meets different
  standards for open science, and addresses the functionality provided by the R implementation,
  worcs . This paper is primarily targeted towards scholars conducting research projects
  in R, conducting research that involves academic prose, analysis code, and tabular
  data. However, the workflow is flexible enough to accommodate other scenarios, and
  offers a starting point for customized solutions. The source code for the R package
  and manuscript, and a list of examplesof WORCS projects , are available at https://github.com/cjvanlissa/worcs
  .'
keywords:
- dynamic document generation
- Open science
- r
- reproducibility
- version control
start: '29'
end: '49'
repository: https://CRAN.R-project.org/package=worcs
repository-code: https://github.com/cjvanlissa/worcs
url: https://github.com/cjvanlissa/worcs
date-released: '2021-02-03'
contact:
- family-names: van Lissa
  given-names: Caspar J.
  email: c.j.vanlissa@uu.nl
  orcid: https://orcid.org/0000-0002-0808-5024
references:
- type: software
  title: methods
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
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  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Imports
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Luraschi
    given-names: Javier
    email: javier@rstudio.com
  - family-names: Ushey
    given-names: Kevin
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    given-names: Joe
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  year: '2022'
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    given-names: Frederik
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  abstract: 'gert: Simple Git Client for R'
  notes: Imports
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    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
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  notes: Imports
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  title: yaml
  abstract: 'yaml: Methods to Convert R Data to YAML and Back'
  notes: Imports
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  - family-names: Stephens
    given-names: Jeremy
  - family-names: Simonov
    given-names: Kirill
  - family-names: Xie
    given-names: Yihui
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  - name: reikoch
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    given-names: Will
  - family-names: O'Connor
    given-names: Brendan
  - family-names: Warnes
    given-names: Gregory R.
  year: '2022'
  url: https://CRAN.R-project.org/package=yaml
- type: software
  title: digest
  abstract: 'digest: Create Compact Hash Digests of R Objects'
  notes: Imports
  authors:
  - family-names: Lucas
    given-names: Dirk Eddelbuettel with contributions by Antoine
    email: edd@debian.org
  - family-names: Tuszynski
    given-names: Jarek
  - family-names: Bengtsson
    given-names: Henrik
  - family-names: Urbanek
    given-names: Simon
  - family-names: Frasca
    given-names: Mario
  - family-names: Lewis
    given-names: Bryan
  - family-names: Stokely
    given-names: Murray
  - family-names: Muehleisen
    given-names: Hannes
  - family-names: Murdoch
    given-names: Duncan
  - family-names: Hester
    given-names: Jim
  - family-names: Wu
    given-names: Wush
  - family-names: Kou
    given-names: Qiang
  - family-names: Onkelinx
    given-names: Thierry
  - family-names: Lang
    given-names: Michel
  - family-names: Simko
    given-names: Viliam
  - family-names: Hornik
    given-names: Kurt
  - family-names: Neal
    given-names: Radford
  - family-names: Bell
    given-names: Kendon
  - family-names: de Queljoe
    given-names: Matthew
  - family-names: Suruceanu
    given-names: Ion
  - family-names: Denney
    given-names: Bill
  - family-names: Schumacher
    given-names: Dirk
  - family-names: Chang.
    given-names: and Winston
  year: '2022'
  url: https://CRAN.R-project.org/package=digest
- type: software
  title: rticles
  abstract: 'rticles: Article Formats for R Markdown'
  notes: Imports
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - 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@rstudio.com
    orcid: https://orcid.org/0000-0003-4474-2498
  - name: R Foundation
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - name: Journal of Statistical Software
  - family-names: Vaidyanathan
    given-names: Ramnath
    email: ramnath.vaidya@gmail.com
  - name: Association for Computing Machinery
  - family-names: Boettiger
    given-names: Carl
    email: cboettig@gmail.com
  - name: Elsevier
  - family-names: Broman
    given-names: Karl
    email: kbroman@gmail.com
  - family-names: Mueller
    given-names: Kirill
    email: kirill.mueller@ivt.baug.ethz.ch
  - family-names: Quast
    given-names: Bastiaan
    email: bquast@gmail.com
  - family-names: Pruim
    given-names: Randall
    email: rpruim@gmail.com
  - family-names: Marwick
    given-names: Ben
    email: bmarwick@uw.edu
  - family-names: Wickham
    given-names: Charlotte
    email: cwickham@gmail.com
  - family-names: Keyes
    given-names: Oliver
    email: okeyes@wikimedia.org
  - family-names: Yu
    given-names: Miao
    email: yufreecas@gmail.com
  - family-names: Emaasit
    given-names: Daniel
    email: daniel.emaasit@gmail.com
  - family-names: Onkelinx
    given-names: Thierry
    email: thierry.onkelinx@inbo.be
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    given-names: Alessandro
    email: ellessenne@gmail.com
    orcid: https://orcid.org/0000-0002-8319-7624
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    given-names: Marc-Andre
    email: marc-andre.desautels@cstjean.qc.ca
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    given-names: Dominik
    email: leutnant@fh-muenster.de
    orcid: https://orcid.org/0000-0003-3293-2315
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    given-names: Oguzhan
    orcid: https://orcid.org/0000-0002-9949-3348
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    given-names: Dalton
    email: dhance@usgs.gov
  - family-names: Nüst
    given-names: Daniel
    email: daniel.nuest@uni-muenster.de
    orcid: https://orcid.org/0000-0002-0024-5046
  - family-names: Uvesten
    given-names: Petter
    email: petter.uvesten.7362@student.lu.se
  - family-names: Campitelli
    given-names: Elio
    email: elio.campitelli@cima.fcen.uba.ar
    orcid: https://orcid.org/0000-0002-7742-9230
  - family-names: Muschelli
    given-names: John
    email: muschellij2@gmail.com
    orcid: https://orcid.org/0000-0001-6469-1750
  - family-names: Hayes
    given-names: Alex
    email: alexpghayes@gmail.com
    orcid: https://orcid.org/0000-0002-4985-5160
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    given-names: Zhian N.
    email: zkamvar@gmail.com
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    given-names: Noam
    email: noam.ross@gmail.com
    orcid: https://orcid.org/0000-0002-2136-0000
  - family-names: Cannoodt
    given-names: Robrecht
    email: rcannood@gmail.com
    orcid: https://orcid.org/0000-0003-3641-729X
  - family-names: Luguern
    given-names: Duncan
    email: duncan.luguern@gmail.com
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    given-names: David M.
    email: dmkaplan2000@gmail.com
    orcid: https://orcid.org/0000-0001-6087-359X
  - family-names: Kreutzer
    given-names: Sebastian
    email: sebastian.kreutzer@aber.ac.uk
    orcid: https://orcid.org/0000-0002-0734-2199
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    given-names: Shixiang
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  title: remotes
  abstract: 'remotes: R Package Installation from Remote Repositories, Including ''GitHub'''
  notes: Suggests
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    given-names: Gábor
    email: csardi.gabor@gmail.com
  - family-names: Hester
    given-names: Jim
    email: jim.hester@rstudio.com
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  title: tinytex
  abstract: 'tinytex: Helper Functions to Install and Maintain TeX Live, and Compile
    LaTeX Documents'
  notes: Suggests
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=tinytex
- type: software
  title: renv
  abstract: 'renv: Project Environments'
  notes: Suggests
  authors:
  - family-names: Ushey
    given-names: Kevin
    email: kevin@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=renv
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=knitr
- type: software
  title: missRanger
  abstract: 'missRanger: Fast Imputation of Missing Values'
  notes: Suggests
  authors:
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    given-names: Michael
    email: mayermichael79@gmail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=missRanger
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=testthat
  version: '>= 2.1.0'

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Top Committers
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cjvanlissa c****a@u****l 390
myname my@e****m 25
Aaron Peikert a****t@p****e 15
yourname y****e@e****m 15
cjvanlissa c****a@t****u 14
Brandmaier b****r@m****e 14
Barbara Vreede b****e@g****m 6
Lamprecht, A.L. (Anna-Lena) a****t@u****l 5
Aaron Peikert a****t@m****m 4
Hugo Gruson h****n@p****m 2
Jeroen Ooms j****s@g****m 2
Yihui Xie x****e@y****e 2
mstruiksma 6****a@u****m 2
Committer Domains (Top 20 + Academic)

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Past Year
  • Issues: 7
  • Pull requests: 2
  • Average time to close issues: about 20 hours
  • Average time to close pull requests: about 3 hours
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
  • cjvanlissa (33)
  • brandmaier (13)
  • aaronpeikert (11)
  • swvanderlaan (7)
  • DominiqueMaciejewski (5)
  • bvreede (4)
  • aschetti (3)
  • bmkramer (2)
  • joph (2)
  • nsunami (1)
  • taktsun (1)
  • StefKirsch (1)
  • kequach (1)
  • marvas74 (1)
  • nehamoopen (1)
Pull Request Authors
  • aaronpeikert (14)
  • olivroy (4)
  • cjvanlissa (3)
  • annalenalamprecht (3)
  • bvreede (3)
  • brandmaier (2)
  • mstruiksma (2)
  • jeroen (2)
  • Bisaloo (1)
  • JesseKaczmarski (1)
  • yihui (1)
Top Labels
Issue Labels
enhancement (8) bug (3) paper (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 917 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 19
  • Total maintainers: 1
cran.r-project.org: worcs

Workflow for Open Reproducible Code in Science

  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 917 Last month
  • Docker Downloads: 21,613
Rankings
Stargazers count: 5.8%
Forks count: 6.0%
Average: 21.2%
Downloads: 28.7%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • credentials * imports
  • digest * imports
  • gert * imports
  • gh * imports
  • methods * imports
  • prereg * imports
  • ranger * imports
  • renv * imports
  • rmarkdown * imports
  • rticles * imports
  • tinytex * imports
  • usethis * imports
  • yaml * imports
  • knitr * suggests
  • missRanger * suggests
  • papaja * suggests
  • remotes * suggests
  • testthat >= 2.1.0 suggests
.github/workflows/check-standard.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
Dockerfile docker
  • rocker/verse 4.0.3 build