Ordination scores and loadings at one level — extract_ordination • gllvmTMB

Ordination scores and loadings at one level

Usage

extract_ordination(fit, level = c("unit", "unit_obs", "B", "W"))

Arguments

fit: A gllvmTMB_multi object.
level: "unit" (between-unit) or "unit_obs" (within-unit). Legacy aliases "B" and "W" are accepted with a deprecation warning.

Value

A list with scores (units or within-unit observations in rows, latent axes in columns) and loadings (traits in rows, axes in columns).

Examples

if (FALSE) { # \dontrun{
  sim <- simulate_site_trait(
    n_sites = 20, n_species = 6, n_traits = 4,
    mean_species_per_site = 4, seed = 1
  )
  fit <- gllvmTMB(
    value ~ 0 + trait +
            latent(0 + trait | site, d = 2) +
            unique(0 + trait | site),
    data = sim$data
  )
  ord <- extract_ordination(fit, level = "unit")
  head(ord$scores)
  ord$loadings
} # }