List profile-ready confidence-interval targets for a fitted model

profile_targets() is an advanced inventory for users who need to diagnose or script profile confidence intervals. Most users should start with confint.gllvmTMB_multi() or a report-ready extractor such as extract_correlations(). This helper tells you which parm labels can be profiled directly.

Usage

profile_targets(object, ready_only = FALSE)

Arguments

object: A fit returned by gllvmTMB().
ready_only: If TRUE, return only rows with profile_ready = TRUE. Default FALSE returns the full inventory.

Value

A data frame with one row per target and the following columns:

parm: User-facing target label, e.g. b_fix[1], sigma_eps, or sd_B[2].
target_class: One of fixed_effect, variance, dispersion, loading_packed, threshold, or scaling.
tmb_parameter: TMB-side parameter name (matches names(fit$opt$par)).
index: 1-based index within the TMB parameter vector. NA for scalars.
estimate: Point estimate on the natural scale (e.g. sigma_eps = exp(log_sigma_eps)).
link_estimate: Point estimate on the optimisation scale (the TMB internal scale).
scale: Either "natural" (after applying the transformation) or "link" (for raw packed entries).
transformation: One of linear_predictor, exp, logit, logit_p_tweedie, lambda_packed, or ordinal_threshold.
target_type: Always "direct" for currently returned rows.
profile_ready: TRUE iff the target can be passed directly to confint(fit, parm = ..., method = "profile").
profile_note: One of ready, tmb_object_required, missing_tmb_parameter, or latent_rotation_ambiguous.

Details

The returned tidy data frame has one row per profile target and records whether the target is profile-ready and, if not, why. Direct targets correspond to a single TMB parameter element (for example b_fix[1], sigma_eps, or sd_B[2]) and can be passed to confint(fit, parm = ..., method = "profile"). Nonlinear derived targets are excluded because their former penalty-profile routes are withheld.

Scope: the controlled vocabulary and direct-profile routing is covered for fitted models with retained TMB objects. Broader target-explicit profile calibration remains future work.

The output uses a controlled vocabulary for direct target classes, transformations, and readiness notes.

Examples

if (FALSE) { # \dontrun{
fit <- gllvmTMB(value ~ 0 + trait + latent(0 + trait | site, d = 1),
                data  = sim$data,
                trait = "trait",
                unit  = "site")
targets <- profile_targets(fit)
head(targets)
profile_targets(fit, ready_only = TRUE)
} # }