Package API

[trannttoan]

No description provided.

[Copilot]

Pull Request Overview

This PR introduces the "Package API" by restructuring the shinymrp package to provide a programmatic interface alongside the existing Shiny GUI. The changes establish a clear object-oriented workflow using R6 classes while consolidating documentation.

• Major refactoring to introduce MRPWorkflow and MRPModel R6 classes for programmatic access
• Consolidation of vignettes from multiple separate guides into comprehensive workflow documentation
• Extensive test updates to align with new API parameter structure

Reviewed Changes

Copilot reviewed 63 out of 96 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
vignettes/workflow.Rmd	New comprehensive workflow vignette demonstrating the complete MRP analysis pipeline
vignettes/getting-started.Rmd	Updated getting started guide with API examples and installation instructions
R/workflow.R	New MRPWorkflow R6 class implementing the main workflow interface
R/model.R	New MRPModel R6 class for individual model management and analysis
tests/testthat/test-fct_model.R	Updated test parameters to match new API structure

Comments suppressed due to low confidence (4)

R/run_app.R:30

• The documentation format is inconsistent. Should use ?golem::get_golem_options instead of \code{?golem::get_golem_options} for consistency with roxygen2 markdown format.

}

tests/testthat/test-fct_model.R:135

• The new parameter structure suggests API changes, but the test coverage for error handling and edge cases with these new parameters may be insufficient. Consider adding tests for invalid parameter combinations.

    show_messages = FALSE,

R/workflow.R:21

• [nitpick] The error message suggests using shinymrp::install_cmdstan() but this may not be clear to users. Consider providing more context about what CmdStan is and why it's required.

  if (is.null(cmdstanr::cmdstan_version(error_on_NA = FALSE))) {