Summarise MCMC Classification Results

Post-processes raw MCMC output from classify_infections into interpretable summaries including posterior probabilities, convergence diagnostics, and a match counting comparison table. Called automatically by MalReBay.

Usage

summarise_results(
  mcmc_results,
  imported_data,
  output_folder = NULL,
  verbose = TRUE,
  prob_threshold = 0.5,
  plots = TRUE
)

Arguments

mcmc_results

A list returned by classify_infections.

imported_data

A list returned by import_data.

output_folder

Path for saving convergence diagnostic plots. NULL skips saving.

verbose

Logical. Print progress messages.

prob_threshold

Numeric in [0, 1]. The posterior probability at or above which a recurrence is classified as "Recrudescence" (below it, "Reinfection"); used to add the Classification column to posterior_probabilities (and comparison). Defaults to 0.5, the natural cutoff under this model's equal 50/50 prior (see @sec-interpretation-probability in the analysis notebook).

plots

Logical. If FALSE, convergence diagnostic plots are not saved to output_folder; the diagnostics themselves are still computed and returned in convergence. Defaults to TRUE.

Value

A named list with posterior_probabilities, comparison, convergence, and mcmc_loglikelihoods. Both posterior_probabilities and comparison include a Classification column derived from prob_threshold.

See also

classify_infections, save_results, MalReBay

Examples

if (FALSE) { # \dontrun{
imported <- import_data()
results  <- classify_infections(imported)
summary  <- summarise_results(results, imported)
} # }