Extract latent variables from gllvm object.
# S3 method for class 'gllvm'
getLV(object, type = NULL, ...)an object of class 'gllvm'.
type of latent variable scores to retrieve from a gllvm object. For models with unconstrained latent variables, defaults to "residual". For models with constrained latent variables, defaults to conditional. Alternatively, "marginal" returns linear combination scores without residual error.
not used
Function retrieves the site scores for a GLLVM. Each type corresponds to a separate term of the model. For a GLLVM with unconstrained latent variables the default is "residual". "Residual" scores represent the error term in concurrent ordination, and are not available for constrained ordination.
For GLLVMs with informed latent variables, "conditional" returns the complete site scores, due to both fixed- and latent effects, where the latent effect is always scaled by the diagonal of the species loadings so that it can be small relative to the fixed-effects. "Conditional" here means conditional on the random-effect i.e. the residual.
Type "marginal" returns linear combination scores, i.e. the site scores only due to fixed-effects. These are available for constrained and concurrent ordination.
If both unconstrained and constrained latent variables are included in the model, type "marginal" returns linear combination scores for constrained latent variables but "residual" scores for unconstrained latent variables.