add_utm_columns         Add UTM coordinates to a data frame
animal_dep              Full unstructured animal-model trait
                        covariance: 'animal_dep(0 + trait | id)'
animal_indep            Independent per-trait animal-model random
                        intercepts: 'animal_indep(0 + trait | id)'
animal_latent           Reduced-rank animal-model latent factors:
                        'animal_latent(id, d = K)'
animal_scalar           Single-shared-variance animal-model random
                        effect: 'animal_scalar(id)'
animal_slope            Animal-model random slope on a continuous
                        covariate
animal_unique           Per-trait independent animal-model random
                        intercepts: 'animal_unique(id)'
block_V                 Build a block-diagonal sampling-variance matrix
                        V
bootstrap_Sigma         Bootstrap covariance, correlation, communality,
                        and ICC summaries
categorical             Baseline-category softmax unordered categorical
                        missing-predictor family
check_auto_residual     Check whether 'link_residual = "auto"' is
                        coherent for this fit
check_gllvmTMB          Check convergence, Hessian, gradients, and
                        interval readiness
compare_Sigma_table     Compare fitted Sigma-table rows with a known
                        truth matrix
compare_dep_vs_two_psi
                        Canonical likelihood-based cross-check for the
                        paired phylogenetic decomposition
compare_indep_vs_two_psi
                        Cheap diagonal cross-check for the paired
                        phylogenetic decomposition (large T)
compare_loadings        Compare two loading matrices after Procrustes
                        alignment
confint.gllvmTMB_multi
                        Confidence intervals for a fitted gllvmTMB
                        model
confint_inspect         Inspect profile confidence-interval shape for a
                        fitted model
confirmatory_lambda     Build a confirmatory 'lambda_constraint' matrix
                        from group membership
cumulative_logit        Cumulative-logit ordered categorical
                        missing-predictor family
dep                     Full unstructured trait covariance: 'dep(0 +
                        trait | g)'
deviance.gllvmTMB_multi
                        Deviance of a fitted gllvmTMB model
diagnose_kernel_separability
                        Diagnose fixed-kernel separability before
                        fitting
diagnostic_table        Extract report-ready tables from diagnostic
                        objects
extract_Gamma           Extract a cross-lineage Gamma block
extract_Omega           Total trait covariance Omega summed across
                        requested tiers
extract_Sigma           Extract the implied trait covariance /
                        correlation at one tier
extract_Sigma_table     Extract a report-ready table of Sigma or
                        correlation entries
extract_coevolution_modules
                        Extract cross-lineage coevolutionary modules
extract_communality     Communality of each trait
extract_correlations    Extract cross-trait correlations
extract_cross_correlations
                        Cross-family correlations between a nominal
                        (multinomial) trait and partners
extract_cutpoints       Extract ordinal-probit cutpoints from a fitted
                        gllvmTMB model
extract_loadings        Extract the trait loading matrix
extract_lv_effects      Predictor effects on latent-score means
extract_ordination      Extract ordination scores and loadings from a
                        fitted multivariate model
extract_phylo_signal    Phylogenetic-signal proportions per trait
extract_proportions     Per-trait proportion-of-variance decomposition
                        across all model components
extract_repeatability   Per-trait repeatability with confidence
                        intervals
extract_residual_cov    Implied trait covariance or correlation
extract_rotated_loadings_table
                        Extract a tidy rotated loading table
fitted.gllvmTMB_multi   Fitted values from a fitted gllvmTMB model
flag_unreliable_loadings
                        Flag loadings whose CI overlaps a "biologically
                        negligible" region
get_crs                 Infer a UTM coordinate reference system
gllvmTMB                Fit multivariate response models from wide or
                        long data
gllvmTMB_check_consistency
                        Run an advanced Laplace-consistency check
gllvmTMB_diagnose       Diagnose a fitted model and suggest next
                        actions
gllvmTMB_julia-methods
                        Methods for Julia bridge fits
gllvmTMB_multi-methods
                        Methods on a fitted gllvmTMB model
gllvmTMB_multi-vcov     Fixed-effect estimates and covariance for a
                        multi-trait fit
gllvmTMB_va-methods     Methods for variational ('integration = "va"')
                        fits
gllvmTMBcontrol         Control parameters for 'gllvmTMB()'
gllvm_julia_fit         Fit a GLLVM with the Julia engine (GLLVM.jl
                        'bridge_fit').
gllvm_julia_setup       Set up JuliaCall and load the GLLVM.jl engine
                        (once per R session).
impute_model            Predictor model for a missing covariate used
                        inside 'mi()'
imputed                 Extract fitted missing-predictor values from a
                        'gllvmTMB' fit
indep                   Per-trait marginal variance: 'indep(0 + trait |
                        g)'
isdm_source             Declare one iSDM source observation model
isdm_sources            Declare the sources of a multi-source
                        integrated model
kernel_latent           Generic dense-kernel covariance keywords
kernel_scalar           Dense-kernel one-shared-variance covariance:
                        'kernel_scalar()'
kernel_unique           Deprecated alias: 'kernel_unique()'
latent                  Latent-factor (reduced-rank) random effect:
                        'latent(0 + trait | g, d = K)'
loading_ci              Confidence intervals on individual entries of
                        the loading matrix
loading_profile         Profile-likelihood curve(s) for entries of the
                        loading matrix
make_cross_kernel       Build a cross-lineage relatedness kernel
make_mesh               Construct an SPDE mesh for gllvmTMB
meta_V                  Known-V meta-analytic random effect (canonical
                        name): 'meta_V(V = V)'
miss_control            Missing-data control for 'gllvmTMB()'
multinomial             Multinomial (baseline-category logit) family
ordinal_probit          Ordinal-probit threshold family for the
                        multivariate engine
pedigree_to_A           Pedigree to additive-genetic relatedness matrix
                        'A'
pedigree_to_Ainv_sparse
                        Sparse pedigree inverse-A via Henderson-Quaas
                        (MCMCglmm-free)
phylo                   Phylogenetic random effect: lme4-bar
                        mode-dispatch wrapper
phylo_dep               Full unstructured phylogenetic trait
                        covariance: 'phylo_dep(0 + trait | species)'
phylo_indep             Per-trait phylogenetic marginal variance:
                        'phylo_indep(0 + trait | species)'
phylo_latent            Reduced-rank phylogenetic latent factors:
                        'phylo_latent(species, d = K)'
phylo_scalar            Single-shared-variance phylogenetic random
                        effect: 'phylo_scalar(species)'
phylo_signal_mi         Phylogenetic-signal diagnostic for a modelled
                        missing predictor
phylo_slope             Phylogenetic random slope on a continuous
                        covariate
phylo_unique            Per-trait independent phylogenetic random
                        intercepts: 'phylo_unique(species)'
plot.gllvmTMB_multi     Plot a fitted multivariate gllvmTMB model
plot.gllvmTMBmesh       Plot a gllvmTMB SPDE mesh
plot.profile_derived    Plot a profile-derived LR curve
plot.profile_loadings   Plot a profile_loadings object (LR U-shape per
                        entry)
plot_Sigma_comparison   Plot Sigma-table estimates against a known
                        truth matrix
plot_Sigma_heatmap      Plot Sigma-table rows as a trait-by-trait
                        heatmap
plot_Sigma_table        Plot report-ready Sigma table rows
plot_anisotropy         Plot the isotropic spatial range from a
                        gllvmTMB model
plot_correlations       Plot pairwise trait correlations with intervals
plot_loadings_confidence_eye
                        Confidence Eye plot for per-species loading
                        uncertainty
plot_rotated_loadings   Plot a rotated loading matrix
predict.gllvmTMB_multi
                        Predict from a fitted gllvmTMB model
predict_cross_covariance
                        Predict pair-specific cross-lineage covariance
predict_missing         Predict the masked (missing) response cells of
                        a gllvmTMB fit
predictive_check        Fitted-model predictive checks for a
                        multivariate 'gllvmTMB' fit
print.gllvmTMB_Sigma_phy_slope
                        Print an augmented latent-slope Sigma
                        extraction
profile_ci_total_variance
                        Profile-likelihood CI for per-trait total
                        variance
profile_cross_rho       Profile fixed cross-lineage rho values
profile_cross_rho_ci    Profile sensitivity interval for the
                        cross-lineage 'rho'
profile_phylo_signal    Profile-likelihood curve(s) for per-trait
                        phylogenetic signal
profile_targets         List profile-ready confidence-interval targets
                        for a fitted model
residuals.gllvmTMB_multi
                        Diagnostic residuals for a multivariate
                        'gllvmTMB' fit
ridge_path              Sweep the loading-ridge penalty and report a
                        stability path
rotate_loadings         Rotate the loadings of a fitted multivariate
                        model
sanity_multi            Print a quick convergence and parameter sanity
                        report
scalar                  One shared trait variance: 'scalar(0 + trait |
                        g)'
screen_control          Control pre-fit response screening
screen_gllvmTMB         Screen candidate responses before fitting a
                        gllvmTMB model
screen_table            Extract tables from a pre-fit screen
simulate.gllvmTMB_multi
                        Simulate new responses from a fitted gllvmTMB
                        model
simulate_site_trait     Simulate a functional-biogeography GLLVM
                        dataset (sites × species × traits)
simulate_unit_trait     Simulate a generic stacked-trait GLLVM dataset
                        (units x observations x traits)
slope_sd_ci             Wald confidence intervals on augmented
                        random-slope standard deviations
spatial                 Spatial random field: lme4-bar mode-dispatch
                        wrapper
spatial_dep             Full unstructured spatial trait covariance:
                        'spatial_dep(0 + trait | coords)'
spatial_indep           Per-trait spatial marginal field:
                        'spatial_indep(0 + trait | coords)'
spatial_latent          Reduced-rank spatial latent factors:
                        'spatial_latent(0 + trait | coords, d = K)'
spatial_scalar          Deprecated alias for one shared spatial-field
                        variance
spatial_unique          Per-trait independent spatial random fields:
                        'spatial_unique(0 + trait | coords)'
standard_errors         Compute standard errors after fitting
suggest_lambda_constraint
                        Suggest a 'lambda_constraint' matrix for a
                        reduced-rank fit
suggest_lambda_constraints
                        Compare several 'lambda_constraint' suggestions
tidy.gllvmTMB_multi     Tidy a fitted gllvmTMB model
traits                  Wide-format trait marker for the 'gllvmTMB()'
                        formula LHS
