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 table.
load_infection_chains( location = getwd(), thin = 1, burnin = 0, chain_subset = NULL )
| location | defaults to current working directory. Where to look for MCMC chains? These are files ending in "_infection_histories.csv" |
|---|---|
| thin | thin the chains by every thin'th sample |
| burnin | discard the first burnin samples from the MCMC chain |
| chain_subset | if not NULL, a vector of indices to only load and store a subset of the chains detected. eg. chain_subset = 1:3 means that only the first 3 detected files will be processed. |
a list with a) a list of each chain as a data table separately; b) a combined data table, indexing each iteration by which chain it comes from
Other load_data_functions:
load_antigenic_map_file(),
load_mcmc_chains(),
load_start_tab(),
load_theta_chains(),
load_titre_dat()
if (FALSE) load_infection_chains(thin=10,burnin=5000,chain_subset=1:3)