valtools helps automate the validation of R packages used in clinical research and drug development: It provides useful templates and helper functions for tasks that arise during project set up and development of the validation framework.

This package is created by the R Package Validation Framework PHUSE Working Group.

For background on the R Package Validation Framework, watch this presentation from RStudio::Global Pharma X Session.

{valtools} is under active development. To get the latest version, install from github:

devtools::install_github("phuse-org/valtools")

{valtools} is intended to be a bolt-on addition to the standard package development process followed by usethis and devtools. All {valtools} functions start with vt followed by a verb/descriptor to make them easy to follow. The most common usage for valtools is to add elements required for validation under the R Package Validation Framework and facilitating validation. See the Starting New Validation Package using {valtools} vignette for more details.

• vt_use_validation() adds the validation infrastructure to an existing R package.
• vt_use_req(), vt_use_test_case(), vt_use_test_code add the requirements, test cases and test code to the validation folder.
• vt_use_change_log() creates a change log in the validation folder
• vt_use_report() creates the validation report Rmd that gets rendered into the validation report.

These functions are helper functions for use within the validation report Rmd.

• vt_path() allows user to base path from the validation directory. Similar idea to the {here} package, but for validation.

• vt_file() allows the user to point to specific files and render them as child documents within the report.

• vt_scrape_* family of functions allows users to scrape information from the validation infrastructure and returns a data.frame.

  • vt_scrape_sig_table() Scrapes the usernames and roles from the validation config file
  • vt_scrape_val_env() Scrapes the environment to give a snapshot of what packages and versions are loaded during validation
  • vt_scrape_change_log() Scrapes the change log
  • vt_scrape_coverage_matrix() Scrapes the coverage roxygen tags in the test case
  • vt_scrape_function_editors() Scrapes the editors of all the functions
  • vt_scrape_requirement_editors() Scrapes the requirement editors
  • vt_scrape_test_case_editors() Scrapes the test case editors
  • vt_scrape_test_code_editors() Scrapes the test code editors
  • vt_scrape_risk_assessment() Scrapes the risk assessments

• vt_kable_* family functions provides an opinionated formatting to the vt_scrape_* functions to help quickly construct the report.

• vt_get_child_files() returns the list of files that are indicated in the validation.yml to be included in the validation report. This allows for batch creation of the dynamic content in the report.

• vt_validate_source() installs the package temporarily and executes the validation report rmd to validate the source code on the current system.
• vt_validate_build() installs the package temporarily, executes the validation report rmd, and compiles it into a bundle for installing.
• vt_validate_install() installs the package temporarily, executes the validation report rmd, and installs the library to the machine.
• vt_validate_installed_package() runs the validation report rmd for a package that was installed using vt_validate_install() for when the environment has changed.

Read the Starting New Validation Package using {valtools} vignette for a high level overview of the functions that exist in {valtools} and their intended uses.

Cheat sheet on how to use the {valtools} R Package

Please note that the {valtools} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.