Load MCMC chains for the antibody kinetics parameters and infection histories from CSV outputs

Reads in all MCMC chains for theta and infection histories from the specified directory matching files ending "_chain.csv", adding in the total number of infections.

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

Arguments

location

Character string path to the directory containing the chain files. Defaults to `getwd()`.

par_tab

Data frame; optional model control table used to select estimated parameters. Defaults to `NULL`.

estimated_only

if TRUE, only returns free model parameters (`par_tab$fixed == 0`) when `par_tab` is supplied. Defaults to `FALSE` for this wrapper.

thin

Integer; keeps every `thin`th saved MCMC sample. Defaults to `1` (no thinning).

burnin

Integer; discards samples with `samp_no <= burnin`. Defaults to `0`.

convert_mcmc

if TRUE, converts the returned parameter chains to `coda::mcmc` objects. Defaults to `FALSE`.

verbose

Logical; whether to print progress messages.

Value

A list with four entries: `theta_chain` and `inf_chain` contain the combined parameter and infection-history chains; `theta_list_chains` and `inf_list_chains` contain the corresponding chains separately. If `convert_mcmc = TRUE`, the parameter chains are converted to `coda::mcmc` objects; the infection-history chains remain data tables.

See also

Other load_data_functions: load_antibody_data(), load_antigenic_map(), load_infection_chains(), load_start_tab(), load_theta_chains()

Examples

if (FALSE) load_mcmc_chains(par_tab=par_tab, estimated_only=TRUE,thin=10,burnin=5000,convert_mcmc=TRUE) # \dontrun{}