bayestransmission (version 0.1.0)

mcmc_to_dataframe: Convert MCMC Parameters to Data Frame

Description

Converts the nested list structure of MCMC parameters from runMCMC output into a tidy data frame format suitable for analysis and visualization.

Usage

mcmc_to_dataframe(mcmc_results)

Value

A data frame with one row per MCMC iteration containing:

• iteration: The iteration number

• insitu_*: In-situ probability parameters

• surv_test_*: Surveillance test parameters

• clin_test_*: Clinical test parameters and rates

• outunit_*: Out of unit infection parameters

• inunit_*: In unit LinearAbx model parameters (base, time, mass, freq, colabx, susabx, susever, clr, clrAbx, clrEver)

• abxrate_*: Antibiotic rate parameters

• loglikelihood: Log likelihood at each iteration

Arguments

mcmc_results

The results object returned by runMCMC(). Must contain a Parameters component and a LogLikelihood component.

Details

The function extracts parameters from the nested list structure and handles missing values gracefully by inserting NA when a parameter is not present. This is particularly useful for creating trace plots and posterior distributions.

Examples

results <- runMCMC(data = simulated.data,
                   modelParameters = LinearAbxModel(),
                   nsims = 10,
                   nburn = 0,
                   outputparam = TRUE,
                   outputfinal = FALSE)
param_df <- mcmc_to_dataframe(results)
head(param_df)