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

Examples

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