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Check a fitted SBT posterior

Source: R/check-fit.R
check_mcmc.Rd

Checks rank-normalized R-hat, bulk and tail effective sample sizes, divergences, maximum-tree-depth hits, and every retained biological state. An MLE is not required; when present, its independently stored validation remains separate. Full-draw validation includes natural mortality at every age. A mortality exception is applied only when explicitly stored with the fit's MCMC acceptance settings or supplied by the caller.

Usage

check_mcmc(
  fit,
  max_rhat = NULL,
  min_bulk_ess = NULL,
  min_tail_ess = NULL,
  divergences = NULL,
  max_treedepth_hits = NULL,
  mortality_exception = NULL,
  cores = 1L,
  state_diagnostics = NULL,
  stop_on_failure = TRUE,
  mode = c("auto", "full", "skip")
)

Arguments

fit

An sbt_fit() containing MCMC draws.

max_rhat, min_bulk_ess, min_tail_ess

Optional sampler thresholds. Values stored with the fit are used by default, followed by 1.01, 400, and 400.

divergences, max_treedepth_hits

Required pathology counts; defaults are zero.

mortality_exception

Optional explicit mortality-exception list.

cores

Number of workers used for full-draw state evaluation.

state_diagnostics

Optional biological-state diagnostics already calculated from this exact posterior in the current completion workflow. This avoids evaluating every draw a second time; normal later calls should leave it NULL and reuse the embedded validation record.

stop_on_failure

Stop when any gate fails. Set to FALSE to retain a rejected posterior and its diagnostics for inspection.

mode

Validation mode. "auto" reuses a matching embedded record and otherwise performs the checks, "full" always performs them, and "skip" returns the fit without checking or creating a record.

Value

The checked sbt_fit, with diagnostics stored in fit$fit$diagnostics$mcmc and full state results in fit$fit$diagnostics$biological_state_posterior. A payload-bound result is stored in fit$validation.

See also

Other fit workflow: check_mle(), sbt_add_bounds(), sbt_add_map(), sbt_add_msy(), sbt_add_parameters(), sbt_add_priors(), sbt_build_object(), sbt_example_fit(), sbt_fit(), sbt_fit_compatibility(), sbt_fit_io, sbt_fit_rebuild(), sbt_fit_report(), sbt_fit_validate(), sbt_fit_validation(), sbt_mcmc(), sbt_obj(), sbt_optimise()

Examples

if (FALSE) { # \dontrun{
fit <- sbt_example_fit()
fit <- sbt_mcmc(fit)
fit <- check_mcmc(fit, mode = "auto")
sbt_fit_validation(fit, scope = "mcmc", require_pass = TRUE)$passes
} # }