One-call diagnostic + biological summary for a gllvmTMB_multi fit

This is the function to call right after fit <- gllvmTMB(...). It rolls up the existing diagnostics (sanity_multi()), the rotation identifiability advisory, and the key biological summaries (correlation diagonals, ICCs, communalities) into a single human- readable report with explicit next-step hints for any WARN signal.

Usage

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

Arguments

object

A gllvmTMB_multi fit.

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).

See also

sanity_multi(), suggest_lambda_constraint(), extract_Sigma(), extract_communality(), compare_dep_vs_two_U() / compare_indep_vs_two_U() for identifiability cross-checks.

Examples

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