Package index

Top-level entry points

Fit a stacked-trait GLLVM

gllvmTMB(): Fit a stacked-trait, multivariate GLLVM
traits(): Wide-format trait marker for the gllvmTMB() formula LHS
gllvmTMBcontrol(): Control parameters for gllvmTMB()
simulate_site_trait(): Simulate a functional-biogeography GLLVM dataset (sites × species × traits)

Covariance keywords

The 3 x 5 keyword grid (correlation x mode)

latent(): Latent-factor (reduced-rank) random effect: latent(0 + trait | g, d = K)
unique_keyword unique: Trait-specific unique variance: unique(0 + trait | g)
indep(): Per-trait marginal variance: indep(0 + trait | g)
dep(): Full unstructured trait covariance: dep(0 + trait | g)
phylo_scalar(): Single-shared-variance phylogenetic random effect: phylo_scalar(species)
phylo_unique(): Per-trait independent phylogenetic random intercepts: phylo_unique(species)
phylo_indep(): Per-trait phylogenetic marginal variance: phylo_indep(0 + trait | species)
phylo_dep(): Full unstructured phylogenetic trait covariance: phylo_dep(0 + trait | species)
phylo_latent(): Reduced-rank phylogenetic latent factors: phylo_latent(species, d = K)
phylo_slope(): Phylogenetic random slope on a continuous covariate
spatial_scalar(): One shared spatial-field variance across traits: spatial_scalar(0 + trait | coords)
spatial_unique(): Per-trait independent spatial random fields: spatial_unique(0 + trait | coords)
spatial_indep(): Per-trait spatial marginal field: spatial_indep(0 + trait | coords)
spatial_dep(): Full unstructured spatial trait covariance: spatial_dep(0 + trait | coords)
spatial_latent(): Reduced-rank spatial latent factors: spatial_latent(0 + trait | coords, d = K)
spde(): Spatial reduced-rank Gaussian random field per trait (Matérn, SPDE/GMRF)
spatial(): Spatial random field: lme4-bar mode-dispatch wrapper
meta_known_V(): Known-V meta-analytic random effect: meta_known_V(value, V = V)

Deprecated keyword aliases

Older keyword names kept for backward compatibility

phylo(): Phylogenetic random effect: lme4-bar mode-dispatch wrapper
phylo_rr(): Reduced-rank phylogenetic random effect (PGLLVM)
gr(): Generic group-with-known-covariance random effect (brms-style)
meta(): Known sampling-error term (brms-style, deprecated alias)
block_V(): Build a block-diagonal sampling-variance matrix V

Response families

ordinal_probit(): Ordinal-probit threshold family for the multivariate engine

Extractors

Recover Sigma, Lambda, repeatability, communality, phylogenetic signal

extract_Sigma(): Extract the implied trait covariance / correlation at one tier
extract_Omega(): Total trait covariance Omega summed across requested tiers
extract_communality(): Communality of each trait (manuscript Eq. 32)
extract_correlations(): Cross-trait correlations with confidence intervals
extract_repeatability(): Per-trait repeatability with confidence intervals
extract_phylo_signal(): Phylogenetic-signal proportions per trait (PGLLVM Eq. 23-25)
extract_proportions(): Per-trait proportion-of-variance decomposition across all model components
extract_residual_split(): Separate OLRE residual variance from the distribution-specific latent residual
extract_ordination(): Ordination scores and loadings at one level
extract_ICC_site(): Site / individual-level ICC per trait (manuscript Eq. 24)
extract_cutpoints(): Extract ordinal-probit cutpoints from a gllvmTMB_multi fit

S3 methods on `gllvmTMB_multi` fits

print(<gllvmTMB_multi>) summary(<gllvmTMB_multi>) print(<summary.gllvmTMB_multi>) logLik(<gllvmTMB_multi>): Methods on a fitted gllvmTMB model
confint(<gllvmTMB_multi>): Confidence intervals on fixed effects of a gllvmTMB_multi fit
tidy(<gllvmTMB_multi>): Tidy a gllvmTMB_multi fit
simulate(<gllvmTMB_multi>): Simulate new responses from a fitted gllvmTMB_multi
predict(<gllvmTMB_multi>): Predict from a gllvmTMB_multi fit
plot(<gllvmTMB_multi>): Plot a fitted multivariate gllvmTMB_multi model

Diagnostics

Evaluate a fitted gllvmTMB_multi model

sanity_multi(): Convergence and parameter sanity report for a gllvmTMB_multi fit
gllvmTMB_diagnose(): One-call diagnostic + biological summary for a gllvmTMB_multi fit
compare_dep_vs_two_U(): Canonical likelihood-based cross-check for the paired phylogenetic decomposition
compare_indep_vs_two_U(): Cheap diagonal cross-check for the paired phylogenetic decomposition (large T)
bootstrap_Sigma(): Parametric bootstrap for Sigma, correlations, communalities, and ICCs
tmbprofile_wrapper(): Profile-likelihood CI for one parameter or linear combination

Loadings (Lambda) and confirmatory factor analysis

Extract, rotate, and constrain the loading matrix

rotate_loadings(): Rotate the loadings of a fitted gllvmTMB_multi model
compare_loadings(): Compare two loading matrices (Procrustes alignment)
suggest_lambda_constraint(): Suggest a lambda_constraint matrix for a reduced-rank GLLVM

Spatial mesh helpers

make_mesh() plot(<sdmTMBmesh>): Construct an SPDE mesh for gllvmTMB
add_utm_columns() get_crs(): Add UTM coordinates to a data frame
plot_anisotropy() plot_anisotropy2(): Plot anisotropy from a gllvmTMB model