# Fill in Missing Species Traits Using a Phylogenetic Tree

## Documentation for package ‘pigauto’ version 0.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'
trees300 | 50 posterior phylogenies for the 300 species in 'avonet300'
tree_full | Example bird phylogeny for the species in 'avonet_full'
with_imputations | Fit a downstream model on every imputed dataset