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https://github.com/workflowr/workflowr

Organize your project into a research website
https://github.com/workflowr/workflowr

git project-management r rmarkdown rstats website workflow

Last synced: 4 days ago
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Organize your project into a research website

Host: GitHub
URL: https://github.com/workflowr/workflowr
Owner: workflowr
License: other
Created: 2016-12-08T02:02:58.000Z (about 8 years ago)
Default Branch: main
Last Pushed: 2024-02-23T17:20:08.000Z (11 months ago)
Last Synced: 2024-08-04T11:01:14.413Z (6 months ago)
Topics: git, project-management, r, rmarkdown, rstats, website, workflow
Language: R
Homepage: https://workflowr.github.io/workflowr
Size: 3.26 MB
Stars: 819
Watchers: 31
Forks: 106
Open Issues: 42
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

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README

        # workflowr: organized + reproducible + shareable data science in R

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

[![CRAN downloads](https://cranlogs.r-pkg.org/badges/workflowr)](https://cran.r-project.org/package=workflowr)

[![DOI](https://zenodo.org/badge/75893305.svg)](https://zenodo.org/badge/latestdoi/75893305)

[![build](https://github.com/workflowr/workflowr/workflows/build/badge.svg)](https://github.com/workflowr/workflowr/actions/workflows/build.yaml)

[![codecov](https://codecov.io/gh/workflowr/workflowr/branch/main/graphs/badge.svg?branch=main)](https://app.codecov.io/gh/workflowr/workflowr)



The workflowr R package helps researchers organize their analyses in a way that

promotes effective project management, reproducibility, collaboration, and

sharing of results. Workflowr combines literate programming (knitr and

rmarkdown) and version control (Git, via git2r) to generate a website containing

time-stamped, versioned, and documented results. Any R user can quickly and

easily adopt workflowr.

For more details, see the [online documentation][workflowr-docs]. For an

example, see the [Divvy data exploration project][divvy]. To explore

reproducible research projects facilitated by workflowr, browse the projects

registered at [workflowr.io][]. To keep up-to-date with the latest workflowr

developments, please join the [workflowr-announce][] mailing list (low-volume,

read-only). For bugs reports, feature requests, and questions, please open an

[Issue][issues].

[workflowr.io]: https://workflowr.io/

[workflowr-announce]: https://groups.google.com/forum/#!forum/workflowr-announce

* [Features](#features)

* [Installation](#installation)

* [Quick start](#quick-start)

* [Attribution](#attribution)

* [Contributing](#contributing)

## Features

* Organized

    * Provides a project template with organized subdirectories

    * Mixes code and results with R Markdown

    * Uses Git to version both source code and results

* Reproducible

    * Displays the code version used to create each result

    * Runs each analysis in an isolated R session

    * Records the session information of each analysis

    * Sets the same seed for random number generation for each analysis

* Shareable

    * Creates a website to present your research results

    * Documents how to host your website for free via [GitHub Pages][] or

    [GitLab Pages][]

    * Creates links to past versions of results

To see a workflowr website in action, see this [video demonstration][video].

For related tools, see [r-project-workflows][].

## Installation

1. Install [R][r]

    * (Recommended) Install [RStudio][rstudio]

    * (Optional) Install [pandoc][] ([Instructions][pandoc-install])

    * (Optional) Install [Git][git]

1. Install workflowr from [CRAN][cran]:

    ```r

    install.packages("workflowr")

    ```

1. Create an account on [GitHub][gh] or [GitLab][gl]

## Quick start

```

library("workflowr")

# Configure Git (only need to do once per computer)

wflow_git_config(user.name = "Full Name", user.email = "email@domain")

# Start a new workflowr project

wflow_start("myproject")

# Build the site

wflow_build()

# Customize your site!

#   1. Edit the R Markdown files in analysis/

#   2. Edit the theme and layout in analysis/_site.yml

#   3. Add new or copy existing R Markdown files to analysis/

# Preview your changes

wflow_build()

# Publish the site, i.e. version the source code and HTML results

wflow_publish("analysis/*", "Start my new project")

```

**Next steps:**

1. Read the full [Getting started vignette][vig-start] to learn how to share

your results online. Alternatively, you could read the [Reproducible research

workshop vignette][vig-workshop]. It covers the same steps, but includes example

code and data to demonstrate some of workflowr's reproducibility features

1. Read the [customization vignette][vig-custom] for ideas on how to customize

your research website

1. Read the [migrating vignette][vig-migrating] for how to integrate workflowr

into your existing project

## Attribution

Workflowr was developed, and is maintained, by John Blischak, a postdoctoral

researcher in the laboratory of [Matthew Stephens][stephens] at [The University

of Chicago][uchicago]. He is funded by a grant from the [Gordon and Betty Moore

Foundation][moore] to MS. [Peter Carbonetto][pcarbo] and [Matthew

Stephens][stephens] are co-authors.

We are very thankful to workflowr [contributors][] for helping improve the

package. We are also grateful for workflowr users for testing the package and

providing feedback---thanks especially to [Lei Sun][lsun], [Xiang

Zhu][xiangzhu], [Wei Wang][nkweiwang], and other members (past and present) of

the Stephens lab.

The workflowr package uses many great open source packages. Especially critical

for this project are the R packages [git2r][], [knitr][], and [rmarkdown][].

Please see the vignette [How the workflowr package works][vig-details] to learn

about the software that makes workflowr possible.

Workflowr is available under the [MIT license][MIT]. For proper attribution,

please cite our [manuscript][workflowr-paper] that describes the software:

> Blischak JD, Carbonetto P, and Stephens M. Creating and sharing reproducible

> research code the workflowr way [version 1; peer review: 3 approved].

> F1000Research 2019, 8:1749 (https://doi.org/10.12688/f1000research.20843.1)

To obtain a BibTeX entry, please run `citation("workflowr")`. Note that

F1000Research publishes not only the original version but also any revisions. To

check for the latest version, please go to the paper's [URL][workflowr-paper].

## Contributing

We welcome community contributions, especially improvements to documentation. To

get started, please read the [contributing guidelines](CONTRIBUTING.md).

Also, please note that this project is released with a [Contributor Code of

Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to

abide by its terms.

[contributors]: https://github.com/workflowr/workflowr/graphs/contributors

[cran]: https://cran.r-project.org/package=workflowr

[divvy]: https://stephenslab.github.io/wflow-divvy/

[gh]: https://github.com

[gl]: https://about.gitlab.com/

[git]: https://git-scm.com/

[git2r]: https://cran.r-project.org/package=git2r

[GitHub Pages]: https://pages.github.com/

[GitLab Pages]: https://about.gitlab.com/stages-devops-lifecycle/pages/

[issues]: https://github.com/workflowr/workflowr/issues

[knitr]: https://github.com/yihui/knitr

[lsun]: https://github.com/LSun

[MIT]: https://opensource.org/licenses/mit-license.php

[moore]: https://www.moore.org/

[nkweiwang]: https://github.com/NKweiwang

[pandoc]: https://pandoc.org/

[pandoc-install]: https://pandoc.org/installing.html

[pcarbo]: https://pcarbo.github.io/

[r]: https://cran.r-project.org

[rmarkdown]: https://rmarkdown.rstudio.com/

[r-project-workflows]: https://github.com/jdblischak/r-project-workflows#readme

[rstudio]: https://posit.co/download/rstudio-desktop/

[stephens]: https://stephenslab.uchicago.edu/

[uchicago]: https://www.uchicago.edu/

[video]: https://www.youtube.com/watch?v=O1wv94sZfvE

[vig-custom]: https://workflowr.github.io/workflowr/articles/wflow-02-customization.html

[vig-details]: https://workflowr.github.io/workflowr/articles/wflow-04-how-it-works.html

[vig-migrating]: https://workflowr.github.io/workflowr/articles/wflow-03-migrating.html

[vig-start]: https://workflowr.github.io/workflowr/articles/wflow-01-getting-started.html

[vig-workshop]: https://workflowr.github.io/workflowr/articles/wflow-09-workshop.html

[workflowr-docs]: https://workflowr.github.io/workflowr/

[workflowr-paper]: https://doi.org/10.12688/f1000research.20843.1

[xiangzhu]: https://github.com/xiangzhu