Unit testing for data-process.R

[SaranjeetKaur]

Use data_ps3_reformulation for unit testing of data-process.R and health-plots.R

This pull request includes several significant changes to the project's configuration files and R scripts to improve automation, code style, and data processing functionalities. The most important changes include adding a pre-commit configuration, enhancing GitHub Actions workflows, and refactoring data processing functions to be more efficient and maintainable.

Configuration and Automation Improvements:

• Added a GitHub Actions workflow to run pre-commit hooks and automatically merge changes if no issues are found.
• Added a pre-commit configuration file to enforce code style and other checks before commits.
• Updated the .Rbuildignore file to include new configuration files and ensure they are ignored during the build process.
• Updated the inst/config/config.yml file to include new grouping variables, weighted variables, and disease prevalence and incidence lists.

Data Processing Refactor:

• Refactored the gen_data_weighted, gen_data_weighted_rf, gen_data_weighted_ds, gen_data_weighted_burden, gen_data_weighted_burden_spline functions to improve efficiency and readability by using dplyr and tidyr functions and incorporating configuration settings.

Dependency Updates:

• Updated the Imports section to include rlang and stringr for improved data manipulation and string handling.

Documentation:

• Updated the documentation for the gen_data_weighted_burden_spline function to reflect the new argument name data_weighted_burden_wide_collapse.

[SaranjeetKaur]

When running devtools::check() it gave (for once):

❯ checking for future file timestamps ... NOTE
  unable to verify current time

0 errors ✔ | 0 warnings ✔ | 1 note ✖

This was resolved following the suggestions on the post:

• Run usethis::edit_r_environ()
• Add _R_CHECK_SYSTEM_CLOCK_=0 to the file
• Save, close file, restart R

After which devtools::check() gives:

0 errors ✔ | 0 warnings ✔ | 0 notes ✔