cdmetapopR 2.0.0 (2026-10-07)

Breaking changes

launch_cdmetapop() has a completely redesigned API. The old signature with separate runvarsDirectory, runvarsFilename, and outputDirectory arguments has been replaced with a new signature that accepts either a RunVars object or a path to an existing run directory. This change enables the new R6 class system and automatic input file writing. Users must update their code to use the new signature (see function documentation for details).

Disease module support: Added comprehensive support for CDMetaPOP’s disease module, including:
- New DiseaseVars R6 class for disease model configuration
- make_diseasevars() Shiny app to generate DiseaseVars.csv templates
- Disease-related columns in PatchVars (disease_file, Env Res, dd1_*/dd2_* transition columns)
- Disease integration in PopVars via implement_disease control
- Validation functions for disease transition rates and cross-field consistency
R6 class system: Implemented R6 classes for all CDMetaPOP input file types:
- ClassVars for age-class specifications
- PatchVars for patch configuration
- PopVars for population batch definitions
- RunVars for simulation run settings
- DiseaseVars for disease model parameters
- All classes include comprehensive validation and helper methods
Read/write functionality:
- read_cdmetapop() reads existing CDMetaPOP input files into R6 objects
- write_cdmetapop() writes R6 objects to CDMetaPOP-formatted CSV files
- Supports all five input file types
New vignette: Added “Building CDMetaPOP input files in R” vignette with comprehensive examples for creating, validating, and launching simulations using the R wrapper

make_classvars(): Refactored age-sex input format, improved Shiny UI
make_patchvars(): Added disease tab with disease-related columns; changed default K and N0 from 0 to 100
make_popvars(): Added disease tab and implement_disease control
make_runvars(): Added ncores option to Shiny UI and output template
launch_cdmetapop(): Enhanced to support disease module and R6 class system
Removed quotes from character fields in CSV output files for CDMetaPOP compatibility