Renaming model measles quarantine and other changes

[gvegayon]

This pull request introduces several updates and improvements to the epiworldR package, focusing on the measles models and developer tooling. The most significant changes are the renaming and deprecation of the ModelMeaslesQuarantine model in favor of ModelMeaslesSchool, enhancements to the ModelMeaslesMixing model interface and documentation, and updates to the underlying C++ code for tracking agent interactions. Additionally, the package version has been incremented and developer environment configurations have been improved.

Model Renaming and Deprecation

• The ModelMeaslesQuarantine model has been renamed to ModelMeaslesSchool, and the old function is now deprecated with a warning to use the new name instead. All relevant code, documentation, and C++ bindings have been updated to reflect this change. (R/ModelMeaslesSchool.R, NAMESPACE, NEWS.md, R/cpp11.R) [1] [2] [3] [4] [5] [6]

Model Interface and Documentation Improvements

• The ModelMeaslesMixing R function interface was refactored to remove the vname parameter and provide sensible defaults for key epidemiological parameters, improving usability and clarity. Documentation was updated to match the new interface and provide more accurate information on model behavior. (R/ModelMeaslesMixing.R) [1] [2] [3] [4] [5]
• The corresponding C++ model constructor was updated to remove the unused virus name parameter, aligning with the R interface changes. (inst/include/epiworld/models/measlesmixing.hpp) [1] [2] [3] [4]

C++ Model Enhancements

• Added a new vector tracking_matrix_date to ModelMeaslesMixing for more precise tracking of agent interaction dates, and refactored the tracking logic for improved accuracy and efficiency. (inst/include/epiworld/models/measlesmixing.hpp) [1] [2] [3]

Versioning and Release Notes

• Incremented the C++ library patch version and updated the package version to 0.9.1.0, with corresponding release notes detailing the changes and deprecation. (inst/include/epiworld/epiworld.hpp, NEWS.md) [1] [2]

Developer Tooling and Environment

• Updated the development Docker image to use R 4.5.1 and improved VSCode devcontainer settings for R development. Also, ensured required tools are installed for GitHub Actions workflows. (.devcontainer/Dockerfile, .devcontainer/.vscode/settings.json, .github/workflows/r.yml) [1] [2] [3]

[Copilot]

Pull Request Overview

This pull request implements several updates to the epiworldR package, primarily focused on renaming and improving the measles models. The most significant change is renaming ModelMeaslesQuarantine to ModelMeaslesSchool with proper deprecation handling, along with interface improvements to ModelMeaslesMixing and various infrastructure updates.

• Rename ModelMeaslesQuarantine to ModelMeaslesSchool with deprecation warning
• Remove vname parameter from ModelMeaslesMixing and provide default values for epidemiological parameters
• Update C++ tracking implementation for more precise agent interaction monitoring

Reviewed Changes

Copilot reviewed 34 out of 34 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/epimodels.cpp	Updates C++ function signatures to match model renames and parameter changes
src/cpp11.cpp	Updates auto-generated C++ bindings for renamed functions and parameter changes
man/*.Rd	Updates documentation cross-references to use new model name
inst/tinytest/test-measlesmixing.R	Removes tests for deprecated vname parameter
inst/include/epiworld/models/measlesquarantine.hpp	Renames class and functions from ModelMeaslesQuarantine to ModelMeaslesSchool
inst/include/epiworld/models/measlesmixing.hpp	Removes vname parameter and improves contact tracking with date information
inst/include/epiworld/epiworld.hpp	Increments C++ library patch version
R/cpp11.R	Updates R function signatures to match C++ changes
R/ModelMeaslesSchool.R	Renames main function and adds deprecation wrapper
R/ModelMeaslesMixing.R	Removes vname parameter and adds default values
NEWS.md	Documents version update and model name change
NAMESPACE	Exports new model name
.github/workflows/r.yml	Installs curl for GitHub Actions
.devcontainer/Dockerfile	Updates R version to 4.5.1
.devcontainer/.vscode/settings.json	Adds VSCode R development settings

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[Copilot]

The parameter count for ModelMeaslesMixing_cpp should be 20, but the actual function signature shows 21 parameters. This mismatch will cause runtime errors when R tries to call the C++ function.

Suggested change

	{"_epiworldR_ModelMeaslesMixing_cpp", (DL_FUNC) &_epiworldR_ModelMeaslesMixing_cpp, 20},
	{"_epiworldR_ModelMeaslesMixing_cpp", (DL_FUNC) &_epiworldR_ModelMeaslesMixing_cpp, 21},

[Copilot]

The default value for contact_rate references prodromal_period, but prodromal_period is defined later in the parameter list (line 125). This will cause an error since R evaluates default values left-to-right and prodromal_period is not yet available.

[Copilot]

Typo in documentation: 'se' should be 'set'.

Suggested change

	#' way to se the contact rate is available, and will be distributed in the
	#' way to set the contact rate is available, and will be distributed in the