Extract implied trait covariance or correlation

Returns the implied trait covariance at level = "unit" or level = "unit_obs". For a reduced-rank plus unique tier this is \(\Sigma_X = \Lambda_X \Lambda_X^\top + \Psi_X\). getResidualCor() returns the corresponding correlation matrix. The canonical snake_case spellings in this package are extract_residual_cov() and extract_residual_cor(), which forward here.

Usage

getResidualCov(fit, level = "unit")

getResidualCor(fit, level = "unit")

Arguments

fit

A fitted multivariate model returned by gllvmTMB(). Admitted engine = "julia" bridge fits expose raw unit-tier loadings and scores; rotated ordinations remain gated for Julia bridge fits.

level

"unit" (between-unit) or "unit_obs" (within-unit). Deprecated aliases "B" and "W" are still accepted with a warning.

Value

An n_traits × n_traits matrix.

See also

extract_Sigma() — the canonical unified API for between-/within-/phylogenetic Sigma at any tier.