Profile-likelihood CI for per-trait phylogenetic signal H^2 — profile_ci_phylo

For fits with phylo_indep(species) and indep(0 + trait | species) but no species-level latent() term, H^2 = sigma2_phy / (sigma2_phy + sigma2_non) is a 2-component ratio profileable via a single linear contrast (log_sd_phy_diag[t] - theta_diag_species[t]).

Usage

profile_ci_phylo_signal(fit, trait_idx = NULL, level = 0.95)

Arguments

fit: A fit returned by gllvmTMB().
trait_idx: Integer index of the trait, or NULL for all.
level: Confidence level. Default 0.95.

Value

A data frame with columns trait, H2, lower, upper, method.

Details

For richer 3-component decompositions (PGLLVM with phylo_latent() plus a species-level latent decomposition with Psi), full profile requires fix-and-refit on the multi-component constraint and remains planned. The current method = "profile" entry point returns the existing numerical delta-method Wald bounds with a clear method = "wald(numeric)" label rather than returning empty bounds.