Package index • samOptiPro

Main functions

test_strategy(): Test and compare MCMC strategies on selected bottleneck nodes

diagnose_model_structure(): Diagnose model structure, dependencies, and sampler time (parameter and family levels)

run_baseline_config(): Run a baseline RW/slice configuration (sequential)

run_hmc_all_nodes(): Run HMC/NUTS on all eligible nodes with slice fallback

assess_performance(): Assess MCMC performance metrics (ESS, R-hat, AE, CE)

assess_performance_vect(): Assess MCMC performance metrics (ESS, R-hat, AE, CE) using vectorised backends

identify_bottlenecks_family(): Identify bottlenecks at the parameter-family level

profile_sampler_times(): Profile sampler times per MCMC sampler

run_structure_and_hmc_test(): Run structural diagnostics and (optional) HMC/NUTS smoke test

test_strategy_family(): Family-based sampler strategy: full HMC if allowed, else surgical on bottlenecks

configure_hmc_safely_bis(): Configure and run HMC/NUTS safely (global / subset / auto)

configure_hmc_safely_parallel(): Configure and run HMC/NUTS safely in true parallel (one chain per worker)

configure_hmc_safely_parallel_bis(): Configure + run HMC/NUTS in parallel (large-model safe, PSOCK)

Plotting & diagnostics

plot_bottlenecks(): Plot MCMC Bottlenecks by Node or Family

plot_bottlenecks_fast(): Fast bottleneck plots (samplers-only) for large models

plot_bottlenecks_index(): Plot diagnostics for stochastic sampler targets (strict) + all-nodes panels

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

plot_convergence_rhat_sampled_fast(): Fast convergence plots for R-hat (samplers-only), thresholded

plot_family_ess_bar(): Family-level ESS bar plot (harmonised style)

plot_family_rhat_bar(): Family-level R-hat bar plot (harmonised style)

plot_mcmc_histograms(): Histograms for ESS, CE, AE, and Rhat

plot_strategies_from_test_result_hmc_fast(): Plot HMC-only strategy comparisons (robust fast path)

compute_diag_from_mcmc(): Build a standard diagnostics table from MCMC samples

compute_diag_from_mcmc_alt(): Scalable diagnostics for large MCMC objects (classic layout, block-wise)

Helpers (internal)

as_mcmc_list_sop(): Convert various sample formats to coda::mcmc.list

generate_all_convergence_and_metric_plots(): Generate all convergence and performance diagnostic plots (HMC/NUTS)

monitors_sampled_from_conf(): Extract sampled-only monitors from a configureMCMC object

monitors_sampled_safe(): One-pass build (uncompiled) + configureMCMC + monitors_sampled

run_baseline_config_parallel(): Run a baseline NIMBLE MCMC configuration in parallel (timing = runMCMC only)

run_baseline_config_parallel_bis(): Run a baseline NIMBLE MCMC configuration in parallel (robust “large-model” variant)

run_custom_mcmc_parallel(): Run a fully customizable NIMBLE MCMC configuration in parallel (baseline / onlySlice / overrides)

run_hmc_all_nodes_parallel(): Run HMC/NUTS on all eligible nodes (with slice fallback), optionally in parallel

run_only_slice_parallel(): Run a slice-only baseline MCMC configuration in parallel

samOptiPro_options(): samOptiPro options constructor