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The workflowr R package helps researchers organize their analyses in a way thatpromotes effective project management, reproducibility, collaboration, andsharing of results. Workflowr combines literate programming (knitr andrmarkdown) and version control (Git, via git2r) to generate a website containingtime-stamped, versioned, and documented results. Any R user can quickly andeasily adopt workflowr.

For more details, see theonline documentation. For anexample, see theDivvy data exploration project. To explorereproducible research projects facilitated by workflowr, browse the projectsregistered atworkflowr.io. To keep up-to-date with the latest workflowrdevelopments, please join theworkflowr-announce mailing list (low-volume,read-only). For bugs reports, feature requests, and questions, please open anIssue.

• Features
• Installation
• Quick start
• Attribution
• Contributing

• 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 viaGitHub Pages orGitLab Pages
  • Creates links to past versions of results

To see a workflowr website in action, see thisvideo demonstration.

For related tools, seer-project-workflows.

1. InstallR

   • (Recommended) InstallRStudio

   • (Optional) Installpandoc (Instructions)

   • (Optional) InstallGit

2. Install workflowr fromCRAN:

   install.packages("workflowr")

3. Create an account onGitHub orGitLab

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 projectwflow_start("myproject")# Build the sitewflow_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 changeswflow_build()# Publish the site, i.e. version the source code and HTML resultswflow_publish("analysis/*", "Start my new project")

Next steps:

1. Read the fullGetting started vignette to learn how to shareyour results online. Alternatively, you could read theReproducible researchworkshop vignette. It covers the same steps, but includes examplecode and data to demonstrate some of workflowr's reproducibility features

2. Read thecustomization vignette for ideas on how to customizeyour research website

3. Read themigrating vignette for how to integrate workflowrinto your existing project

Workflowr was developed, and is maintained, by John Blischak, a postdoctoralresearcher in the laboratory ofMatthew Stephens atThe Universityof Chicago. He is funded by a grant from theGordon and Betty MooreFoundation to MS.Peter Carbonetto andMatthewStephens are co-authors.

We are very thankful to workflowrcontributors for helping improve thepackage. We are also grateful for workflowr users for testing the package andproviding feedback---thanks especially toLei Sun,XiangZhu,Wei Wang, and other members (past and present) ofthe Stephens lab.

The workflowr package uses many great open source packages. Especially criticalfor this project are the R packagesgit2r,knitr, andrmarkdown.Please see the vignetteHow the workflowr package works to learnabout the software that makes workflowr possible.

Workflowr is available under theMIT license. For proper attribution,please cite ourmanuscript that describes the software:

Blischak JD, Carbonetto P, and Stephens M. Creating and sharing reproducibleresearch 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 runcitation("workflowr"). Note thatF1000Research publishes not only the original version but also any revisions. Tocheck for the latest version, please go to the paper'sURL.

We welcome community contributions, especially improvements to documentation. Toget started, please read thecontributing guidelines.Also, please note that this project is released with aContributor Code ofConduct. By participating in this project you agree toabide by its terms.