workflowr

The goal of the workflowr package is to make it easier for researchers to organize their projects and share their results with colleagues. If you are already writing R code to analyze data, and know the basics of Git and GitHub, you can start taking advantage of workflowr immediately. In a matter of minutes, you can create a research website like this.

WARNING: workflowr is still in the early stages of development, so there will potentially be major changes between versions. Thus make sure to upgrade if necessary and look over the documentation. The good news is that any site you create will not be affected by these changes and will continue to function with new versions of the workflowr functions. If you find any problems, or would like to suggest new features, please open an Issue.

Installation

workflowr is hosted in a GitHub repository. To install or upgrade workflowr, run the following in R:

# install.packages("devtools") 
devtools::install_github("jdblischak/workflowr", build_vignettes = TRUE)

Why use workflowr?

First, hopefully you don't need much convincing to write your analyses in R Markdown. It allows you to combine your R code, text, and figures in the same document! See the website to learn about all the cool features. Second, building a website with the rmarkdown package (as opposed to using knitr to produce Markdown files and passing these to a static site generator) enables you to use all the latest R packages (e.g. htmlwidgets) directly in your analyses. Third, the workflowr package provides functions to make it easier for a researcher to maintain a version-controlled R Markdown website:

• A function to start a project with all the necessary files (see ?wflow_start)
• Includes an R Markdown template that will automatically insert the date and most recent Git commit ID (i.e. SHA1) at the top of the file to aid reproducibility (see ?wflow_open)
• Saves generated figures into an organized directory structure
• A function to only build new and updated files (analogous to a Makefile) so that long-running files do not have to be constantly re-run every time the site is built (or rely on caching, which can easily cause reproducibility headaches especially as a project grows) (see ?wflow_build)
• A function to commit the website files to Git, ensuring that they are in sync with the latest committed version of the corresponding R Markdown files (see ?wflow_commit)

Documentation

The following vignettes are available. You can open these locally from R after you've installed the package, or view the vignette online by clicking on the title in the table below.

News

See the file NEWS.md to learn about recent updates.

Credits

workflowr was developed, and is maintained, by John Blischak, a postdoctoral researcher in the laboratory of Matthew Stephens at The University of Chicago. He is funded by a grant from the Gordon and Betty Moore Foundation to MS.

The workflowr package uses many great open source packages. Most importantly it depends on the R packages rmarkdown, which is responsible for providing the infrastructure to convert a collection of R Markdown files into a static website, and git2r, which enables running Git commands from R. Furthermore it relies on the GitHub Pages service for hosting the websites for free. See DESCRIPTION for the full list of R packages used and the vignette that describes the details of how workflowr works.

License

workflowr is available under the MIT license. See the files DESCRIPTION and LICENSE for more details.

Pronunciation

It is common for R packages to end with an "r", and I tend to pronounce this as if it was "er" because I personally find this the easiest. Thus I pronounce the package "workflow + er". Other equally as good options are "workflow + R" or "work + flower".