getResidualCov retrieves the residual covariance matrix; this was designed when gllvm could only include simple row-effects, and does not account for the variation due to the row-effects. However, when row effects (or other random effects, for that matter) are included, these do scale the species' covariance, and should thus be accounted for.
There are different ways to better facilitate extracting the correct associations, we could have something like getTotalCov = getRowCov + getEnvironCor + getResidualCov or just include the row-effect variance in the getResidualCov.
getResidualCovretrieves the residual covariance matrix; this was designed when gllvm could only include simple row-effects, and does not account for the variation due to the row-effects. However, when row effects (or other random effects, for that matter) are included, these do scale the species' covariance, and should thus be accounted for.There are different ways to better facilitate extracting the correct associations, we could have something like
getTotalCov = getRowCov + getEnvironCor + getResidualCovor just include the row-effect variance in thegetResidualCov.