Added simulation_mode (deterministic/stochastic) and nrep support in
configuration parsing and run metadata.
Improved stochastic reproducibility: provided random_seed is honored, and a
seed is generated/stored when missing.
Updated stochastic transition splitting to use binomial draws for integer
compartment flows (n_EIpresymp, n_IsympH, n_HR).
Improved metapopulation infection-flow indexing consistency for destination-
specific force of infection in n_SE_eff and n_VE_eff.
Added bounded vaccination and transition safeguards to reduce overdraw risks (for example, capping applied vaccination by available susceptible count and guarding zero effective population in force-of-infection calculations).
Added integer row allocation for stochastic mixing flows (S and V) using
floor-plus-residual adjustment so row totals are conserved.
Added regression tests for stochastic seed behavior, nsim * nrep instance
counts, and row-allocation conservation checks for S/V mixing.
Enhanced results helper APIs:
MetaRVMResults$plot() now provides direct trajectory plotting before
summarization.MetaRVMSummary$plot() now supports instance-trajectory plotting.summarize() uses a more efficient single-pass grouped aggregation.Subpopulation categories are now user-defined from
population_data$initialization; non-reserved columns are detected
automatically.
Improved checkpoint restore behavior in parse_config(): when
restore_from is provided, population_data$initialization can be used as
mapping-only metadata (without N, S0, I0, etc.).
Improved validation messages for category filters: invalid category names now list available categories, and invalid category values now list valid values for the selected category.
Improved format_metarvm_output() handling of population_id and dynamic
column selection for user-defined categories.
Updated documentation and vignettes to reflect user-defined subpopulation categories and checkpoint restore behavior.