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Project setup and git workflow

Setup Development Environment

  • install git
  • clone this repository
  • open the rstudio project
  • install dependencies with renv::restore()

Project Setup Troubleshooting

If you’re not using Rstudio: start R with the root folder of the project as working directory. renv should be loaded automatically and you should see a message like Project '...' loaded. [renv 1.1.5] and you should be able to use renv::restore(). If renv is not automatically loaded use source("renv/activate.R") to load it.

Project Structure

Reusable functions, methods, etc. will be available as an r-package (built from this repository), that can be tested, built, installed, and distributed. Bespoke code for the simulation study will be included in the directory scripts.

Contribute Code / git workflow

To contribute code:

  1. switch to the main branch git checkout main
  2. make sure you are on the latest version of the main branch git pull main
  3. create a new branch from there git checkout -b <new_branch_name> (replace with the name of your branch)
  4. write your code
  5. Run renv::status() to check if any pacakges need to be installed, updated or added to renv. If necessary use renv::snapshot to add packages you installed to renv or renv::restore if you are missing pacakges others have added.
  6. run devtools::document() to generate documentation and update DESCRIPTION and NAMESPACE
  7. run devtools::test() and devtools::check(), if there are any errors, fix them and iterate from step 5. if all errors are taken care of continue to 8.
  8. commit your code to git through the Rstudio userinterface or with git add . followed by git commit -m "<one-line description of the changes>"
  9. push your code to github with git push -u origin <new_branch_name> for the first time and just git push afterwards
  10. to merge code into the main branch, open a pull request on github. Navigate to your branch use the “Compare & pull request” button.

Coding Style

Please approximately keep to the tidyverse style guide to keep the code easily readable.

Roxygen documentation

Documentation and package metadata are automatically generated with the roxygen2 package. You can add the roxygen tags in r-studio with Code > Insert Roxygen Skeleton. When using functions from other packages, also insert an @importFrom <package> <function1> <function2> ... tag. (See R/utility_functions.R for an example.)

Please also add examples to your function. When adding examples, please ensure that they run without error, since examples are checked when building the package.

Package Dependencies

If dependencies are not automatically added to DESCRIPTION from roxygen tags by running devtools::document(), please add them manually. The most appropriate field will most often be Imports.