https://github.com/phuse-org/valtools
Validation framework for R packages used in clinical research and drug development.
https://github.com/phuse-org/valtools
Last synced: 4 months ago
JSON representation
Validation framework for R packages used in clinical research and drug development.
- Host: GitHub
- URL: https://github.com/phuse-org/valtools
- Owner: phuse-org
- License: other
- Created: 2020-10-21T13:07:58.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-11-05T01:30:37.000Z (5 months ago)
- Last Synced: 2024-11-05T01:30:54.469Z (5 months ago)
- Language: R
- Homepage: https://phuse-org.github.io/valtools/
- Size: 6.92 MB
- Stars: 51
- Watchers: 13
- Forks: 10
- Open Issues: 41
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
- jimsghstars - phuse-org/valtools - Validation framework for R packages used in clinical research and drug development. (R)
README
[](https://github.com/phuse-org/valtools/actions/workflows/R-CMD-check.yaml)
[](https://codecov.io/gh/phuse-org/valtools?branch=main)
[](https://opensource.org/licenses/MIT)
# valtools 
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](https://advance.phuse.global/display/WEL/R+Package+Validation+Framework).
For background on the `R Package Validation Framework`, watch [this presentation](https://www.rstudio.com/resources/rstudioglobal-2021/r-package-validation-framework/) from RStudio::Global Pharma X Session.
## Installation
To install the most recent version officially released on GitHub, use:
```
remotes::install_github("phuse-org/valtools", ref = remotes::github_release())
```
To install the latest development version, use:
```
remotes::install_github("phuse-org/valtools", ref = "develop")
```
## Usage
{valtools} is intended to be a bolt-on addition to the standard package development process followed by [usethis](usethis.r-lib.org) and [devtools](https://devtools.r-lib.org/). 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}`](vignettes/starting-validated-package.Rmd) vignette for more details.
#### Adding Validation Content
- `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.
#### Authoring A 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.
#### Validating
- `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.
## Vignettes
Read the [`Starting New Validation Package using {valtools}`](vignettes/starting-validated-package.Rmd) vignette for a high level overview of the functions that exist in {valtools} and their intended uses.
## Cheat Sheet
Cheat sheet on how to use the {valtools} R Package
## Code of conduct
Please note that the {valtools} project is released with a [Contributor Code of Conduct](CONDUCT.md). By contributing to this project, you agree to abide by its terms.