Searches the given working directory for MCMC outputs from serosolver, loads these in, subsets for burn in and thinning, and formats as both lists and a combined data frame.
load_theta_chains( location = getwd(), par_tab = NULL, unfixed = TRUE, thin = 1, burnin = 0, convert_mcmc = TRUE )
| 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) |
a list with a) a list of each chain separately; b) a combined data frame, indexing each iteration by which chain it comes from
Other load_data_functions:
load_antigenic_map_file(),
load_infection_chains(),
load_mcmc_chains(),
load_start_tab(),
load_titre_dat()
if (FALSE) load_theta_chains(par_tab=par_tab, unfixed=TRUE,thin=10,burnin=5000,convert_mcmc=TRUE)