Parse results from raw EpiFusion object into a R object with infection, Rt, cumulative infection and parameter posteriors — extract_posterior

This function discards the burn-in from the MCMC samples enclosed in a raw EpiFusion object. The posterior samples, and Rhat and ESS statistics for the parameters of the analysis, are stored in a list. Mean values, and HPD intervals for each trajectory type (infections, Rt, cumulative infections and, if applicable, modelled cases) and parameter are provided in the result. To save the posterior samples of each, set include_samples to TRUE (although doing this may made your object very large)

extract_posterior_epifusion(
  raw_epifusion,
  burn_in,
  discard_chains = NA,
  include_samples = FALSE
)

Arguments

raw_epifusion: raw EpiFusion object
burn_in: proportion (as a decimal) of each chain to discard as burn in
discard_chains: (optional) integer vector of chain IDs to discard in the posterior if there were non convergent chains
include_samples: (optional) boolean specifying whether to save the posterior samples in the output object (as opposed to just means and HPDs)

Value

a list of R compatible EpiFusion output objects with burnin discarded