avonet300               AVONET morphological and ecological trait data
                        for 300 bird species
avonet_full             Full AVONET morphological and ecological trait
                        data for 9,993 bird species
build_phylo_graph       Build a phylogenetic graph representation from
                        a tree
calibration_df          Compute calibration data for probability
                        predictions
compare_methods         Compare BM baseline and pigauto methods across
                        replicates
confusion_matrix        Compute a confusion matrix for categorical or
                        binary predictions
cross_validate          k-fold cross-validation for pigauto trait
                        imputation
ctmax_sim               Simulated multi-observation-per-species CTmax
                        data
evaluate                Evaluate a fitted pigauto model on its test set
evaluate_imputation     Evaluate imputation performance against known
                        values
fit_baseline            Fit the phylogenetic baseline
fit_pigauto             Fit a pigauto model for trait imputation
impute                  Impute missing phylogenetic traits (convenience
                        wrapper)
load_pigauto            Load a saved pigauto model
make_missing_splits     Split cells into train/val/test for imputation
                        evaluation
mask_missing            Create an observed/missing mask matrix
multi_impute            Generate experimental stochastic completion
                        datasets
multi_impute_analysis   Analysis-aware multiple imputation for narrow
                        regression models
multi_impute_trees      Posterior-tree prediction sensitivity
pigauto_report          Generate an HTML benchmark report from a
                        pigauto fit
plot.pigauto_benchmark
                        Plot a pigauto benchmark
plot.pigauto_fit        Plot diagnostics for a fitted pigauto model
plot.pigauto_pred       Plot predictions from a pigauto model
plot_comparison         Forest-plot style comparison of benchmark
                        results
plot_history_gg         Plot training history (ggplot2, deprecated)
plot_uncertainty        Plot uncertainty ribbons for imputed trait
                        values
pool_mi                 Pool downstream model fits across multiple
                        imputations (Rubin's rules)
predict.pigauto_fit     Impute missing traits using a fitted pigauto
                        model
preprocess_traits       Preprocess trait data: align to tree, encode
                        into latent space
pull_gbif_centroids     Fetch species range-centroid covariates from
                        GBIF
pull_worldclim_per_species
                        Fetch per-species bioclim covariates from
                        WorldClim v2.1
read_traits             Read trait data from a CSV file or data frame
read_tree               Read a phylogenetic tree from a file
save_pigauto            Save a fitted pigauto model
simulate_benchmark      Run a simulation benchmark for pigauto
simulate_non_bm         Simulate non-BM trait data for benchmarking
suggest_next_observation
                        Suggest which cell to observe next to maximise
                        imputation precision
summary.pigauto_fit     Summary method for pigauto_fit objects
tree300                 Example bird phylogeny for the 300 species in
                        'avonet300'
tree_full               Example bird phylogeny for the species in
                        'avonet_full'
trees300                50 posterior phylogenies for the 300 species in
                        'avonet300'
with_imputations        Fit a downstream model on every imputed dataset
