load_mcmc_chains: Combine theta and infection history chains

In adamkucharski/serosolver: Inference Framework for Serological Data

Combine theta and infection history chains

Description

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

Usage

load_mcmc_chains(
  location = getwd(),
  par_tab = NULL,
  estimated_only = FALSE,
  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
estimated_only	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_antibody_data(), load_antigenic_map_file(), load_infection_chains(), load_start_tab(), load_theta_chains()

Examples

## Not run: load_mcmc_chains(par_tab=par_tab, estimated_only=TRUE,thin=10,burnin=5000,convert_mcmc=TRUE)

adamkucharski/serosolver documentation built on April 13, 2024, 10:24 a.m.