Added opt-in pMCMC output modes that reduce runtime and memory use when full state trajectories are not required. Existing calls retain the previous full-output behaviour by default; use output_level = "minimal", save_state = FALSE, and save_trajectories = FALSE for the smallest output.
Bounded fitted log_init_EIR proposals and corrected their prior specification, improving the reliability of initial = "fitted" runs.
Added staged articles for preparing data and configuration, tuning pMCMC, and assessing confirmation and production chains.
Added user controls for ODE absolute tolerance, relative tolerance, and the maximum number of ODE steps.
anatembea 1.0 (accepted manuscript freeze)
Frozen reproducibility point for the accepted ANC pMCMC manuscript, published in The Lancet Microbe.