Skip to contents

Diagnose a fitted model and suggest next actions

Source: R/diagnose.R
gllvmTMB_diagnose.Rd

This is the human-readable diagnostic to call right after fit <- gllvmTMB(...). It combines the quick numerical screen (sanity_multi()), the rotation identifiability advisory, and key biological summaries (correlation diagonals, ICCs, communalities) into a single report with explicit next-step hints for any WARN signal. Use check_gllvmTMB() when you need the same fit-health checks as a stable table for scripts or reports.

Usage

gllvmTMB_diagnose(
  object,
  gradient_thresh = 0.01,
  se_thresh = 100,
  big_corr_thresh = 0.5,
  verbose = TRUE
)

Arguments

object

A fit returned by gllvmTMB().

gradient_thresh, se_thresh

Forwarded to sanity_multi().

big_corr_thresh

Threshold above which a Sigma_B correlation off-diagonal is flagged as worth highlighting. Default 0.5.

verbose

If TRUE (default), prints the report. Always returns the structured list invisibly.

Value

Invisibly a list with components: sanity (the sanity_multi() flags), rotation (rotation-advisory list), Sigma_B, Sigma_W, ICC_site, communality_B, communality_W, and hints (character vector of suggested actions).

Details

Scope: first-line convergence, Hessian, standard-error, restart, and rotation diagnostics. It reports risks and summaries but does not replace profile, bootstrap, or simulation calibration. Target-explicit validation will decide which interval warnings can be promoted to broader guarantees.

See also

check_gllvmTMB(), sanity_multi(), suggest_lambda_constraint(), extract_Sigma(), extract_communality(), compare_dep_vs_two_psi() / compare_indep_vs_two_psi() for identifiability cross-checks on the paired phylogenetic fit.

Examples

if (FALSE) { # \dontrun{
fit <- gllvmTMB(value ~ 0 + trait + latent(0 + trait | site, d = 2),
                data = dat, trait = "trait", unit = "site")
gllvmTMB_diagnose(fit)
} # }