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hestia 0.1.0

• Stan fitting and draw extraction now use flexstanr. Configure automatic, scheduler-aware within-chain threading with stan_options(threading = TRUE).
• First release.
• Fit Bayesian compartmental infection models from individual-level outcome data, using Stan via ‘rstan’. Models are composed from an infection process and an observation process and fit with a single call.
• Infection-process building blocks: transmit() and progress() define transitions, assembled with make_infection_model(). Susceptible-infected- recovered (SIR), split symptomatic/asymptomatic (SIIR), and similar multi-compartment structures are supported.
• make_observation_model() defines the observation process (per-compartment detection probabilities for one or more tests).
• run_model() fits the assembled model to the data and returns posterior draws on the natural (model) scale.
• get_transmission_details() exposes the parameter structure of an infection model.
• Bundled simulated datasets and fitted-draw fixtures for examples and the vignettes: sir, sir_cov, siir, and the sir_res, sir_cov_res, siir_res posterior draws.
• Vignettes: “SIR” and “multiple infection compartments”.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.