Create MCMC Diagnostics Report — create_mcmc_diagnostics_report • pharmhand

Generates a comprehensive MCMC diagnostics report including trace plots, density plots, convergence assessment, and summary statistics.

Usage

create_mcmc_diagnostics_report(
  fit,
  parameters = NULL,
  rhat_threshold = 1.01,
  ess_threshold = 100,
  title_prefix = "MCMC Diagnostics"
)

Arguments

fit: A brmsfit object from brms package
parameters: Character vector of specific parameters to analyze. If NULL, selects parameters starting with "b_", or the first 5 parameters if no "b_" parameters exist.
rhat_threshold: Numeric. R-hat threshold for convergence
ess_threshold: Numeric. Minimum ESS threshold
title_prefix: Character string for report section titles

Value

A list containing:

trace_plots: List of trace plot ClinicalPlot objects
density_plots: List of density plot ClinicalPlot objects
convergence_assessment: Convergence assessment results
diagnostic_summary: Data frame with key diagnostics

Examples

if (FALSE) { # \dontrun{
report <- create_mcmc_diagnostics_report(fit)
report$trace_plots[[1]]  # Access first trace plot
report$convergence_assessment$recommendations
} # }