Combine theta and infection history chains

Reads in all MCMC chains for theta and infection histories from the specified directory, adding in the total number of infections

load_mcmc_chains(
  location = getwd(),
  par_tab = NULL,
  unfixed = TRUE,
  thin = 1,
  burnin = 0,
  convert_mcmc = FALSE
)

Arguments

location	defaults to current working directory. Gives relative file path to look for files ending in "_chain.csv"
par_tab	if not NULL, can use this to only extract free model parameters
unfixed	if TRUE, only returns free model parameters (par_tab$fixed == 0) if par_tab specified
thin	thin the chains by every thin'th sample
burnin	discard the first burnin samples from the MCMC chain
convert_mcmc	if TRUE, converts everything to MCMC objects (from the `coda` R package)

Value

a list of the concatenated and individual chains (4 elements, either data frames of coda::mcmc objects)

See also

Other load_data_functions: load_antigenic_map_file(), load_infection_chains(), load_start_tab(), load_theta_chains(), load_titre_dat()

Examples

if (FALSE) load_mcmc_chains(par_tab=par_tab, unfixed=TRUE,thin=10,burnin=5000,convert_mcmc=TRUE)