README.md

In windyzn/kidney-manuscript: The longitudinal association of urinary vitamin D binding protein loss with kidney dysfunction in a cohort at risk for type 2 diabetes.

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Explanation of project folders and files

This part of the README details how this research directory is structured, how files should be run, and what the different files do. The layout and setup of this project was designed for using RStudio and devtools. It is set up this way to make it easy for others to run your code and analyses for themselves and to skaffold onto devtools (used for R package development) because it is well documented and actively maintained. See the excellent R for Data Science online book for more details on how to work with this directory format.

Typical commands used in this workflow include:

• Ctrl-Shift-L (devtools::load_all())
• Ctrl-Shift-K (rmarkdown::render('file.Rmd'))

For more detail on using this project workflow, see prodigenr.

To install all the packages necessary for this project (only if usethis::use_package("packagename") has been used often), run this command while in the project:

devtools::install_dev_deps()

General folder details

The project directory is generally structured with the following folders:

• Base folder (./)
• R/
• doc/
• data/
• .git

The base folder contains a few files:

• .gitignore tells Git to ignore certain files from being tracked and prevents them from entering the version control history.
• .Rbuildignore tells devtools which files to not include when running functions such as devtools::load_all().
• DESCRIPTION is a standard file that includes metadata about your project, in a machine readable format for others to obtain information on about your project. It provides a description of what the project does and most importantly what R packages your project uses on.
• The .Rproj file dictates that the directory is a RStudio project. Open the project by opening this file.

All subsequent folders have their own README inside. See them for more details.

Resource

Check out the prodigenr online documentation for details on this setup and workflow. As this layout is also based on R packages, check out the online book on R packages to learn more about how to make the most use out of this project layout (and why prodigenr structures it this way).

windyzn/kidney-manuscript documentation built on May 8, 2019, 5:45 p.m.