Plot convergence diagnostics (R-hat & traces) with family-level R-hat bars

ECDF plots are removed. Only requested items are produced and saved.

Usage

plot_convergence_checks(
  samples,
  out_dir = "outputs/diagnostics",
  top_k_rhat = 12L,
  top_k_aelow = 12L,
  runtime_s = NULL,
  rhat_ref = 1.05,
  make_rhat_hist = TRUE,
  make_traces_rhat = TRUE,
  make_traces_ae = TRUE,
  make_rhat_family_bars = TRUE
)

Arguments

samples

coda::mcmc.list.

out_dir

Output directory (PDF & PNG).

top_k_rhat

Number of targets for "worst R-hat" traces.

top_k_aelow

Number of targets for "worst AE (low ESS/s)" traces.

runtime_s

Total runtime in seconds (optional; used to compute CE if needed).

rhat_ref

Reference R-hat threshold (default 1.01).

make_rhat_hist

Logical – global R-hat histogram.

make_traces_rhat

Logical – traces/densities for worst R-hat.

make_traces_ae

Logical – traces/densities for worst AE (low ESS/s).

make_rhat_family_bars

Logical – bars of median R-hat by family.

Value

(Invisibly) a list with created ggplots/tables.