add roxygen style documentation and vignettes

[Zhenglei-BCS]

@JensBaalkilde , I opened the pull request but please to not yet pull to the master yet.

Summary of Repository Transformation to Roxygen Style with Devtools Workflow

1. Documentation Conversion

Converting .Rd Files to Roxygen Comments

• Used Rd2roxygen package to convert existing .Rd documentation files to roxygen2-style comments
• Placed roxygen comments directly above corresponding function definitions in R source files
• Fixed issues with empty tags and incomplete conversions manually

Enhancing Roxygen Documentation

• Added proper @param, @return, @examples, and other tags to all functions
• Fixed S3 method documentation by adding proper @export tags

Package-Level Documentation

• Created proper package documentation using the "_PACKAGE" approach
• Fixed duplicate alias issues between package documentation and function documentation
• Added comprehensive package description, imports, and metadata

2. NAMESPACE Management

Converting Static NAMESPACE to Roxygen-Generated

• Replaced the manually maintained NAMESPACE file with roxygen-generated one
• Added proper @export tags to all exported functions
• Added @importFrom and @import tags for package dependencies
• Ensured S3 methods were properly exported with @export tags

3. Vignettes Management

Converting Examples to Vignettes

• Created vignettes to showcase package functionality by extracting examples from existing documentation
• Potentially we could move complex examples from function documentation to vignettes
• Fixed example execution issues in documentation

4. Package Structure Modernization

Implementing Devtools Workflow

• Adopted devtools::document() for documentation generation
• Used devtools::check() for package validation
• Used devtools::test() for running unit tests
• Set up devtools::build_vignettes() for vignette building

5. GitHub Pages Integration

Setting Up Package Website

• Used pkgdown to generate a package website

This transformation has modernized the package development workflow, making it easier to maintain, extend, and document the package in the future. The roxygen2-based documentation system ensures that code and documentation stay in sync, while the devtools workflow simplifies package development tasks. The GitHub Pages integration provides accessible documentation for users of the package.

[Zhenglei-BCS]

I opened pull request because I cannot create an issue within a fork.

[Zhenglei-BCS]

Link to Notes

Need to solve before merging (talk to Jen):

• encounter issues when using sandwich methods.

• Do we need the cache folder to build the R package?

[Zhenglei-BCS]

Further improvements $\rightarrow$ open another issue:

• In the future we could configure GitHub Actions to automatically build and deploy the website
• R folder can be organized by group functions with similar application scenario together.

[Zhenglei-BCS]

I made a few changes to the functions to pass CRAN check. However, one important change is in the getFctDerivx Function:

I assumed transfe(e) should be log(e) based on the context, but you should verify this is correct. If transfe is supposed to be a different function. I cannot find a definition within or outside the package.

[Zhenglei-BCS]

The R CMD check action has been passed, however, using internal functions from drc package is remaining a note in the check output. We can either get around this by adding eval(parse) wrapper or directly pull the internal functions into this repo, or try to use the upper level functions instead if possible.

[JensBaalkilde]

Great job on getting documentation up to date and addressing issues!