load_theta_chains: Load MCMC chains for theta

In seroanalytics/serosolver: Inference Framework for Serological Data

Load MCMC chains for theta

Description

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.

Usage

load_theta_chains(
  location = getwd(),
  par_tab = NULL,
  estimated_only = TRUE,
  thin = 1,
  burnin = 0,
  convert_mcmc = TRUE
)

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 with a) a list of each chain separately; b) a combined data frame, indexing each iteration by which chain it comes from

See Also

Other load_data_functions: load_antibody_data(), load_antigenic_map_file(), load_infection_chains(), load_mcmc_chains(), load_start_tab()

Examples

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

seroanalytics/serosolver documentation built on Aug. 18, 2024, 12:46 p.m.