pigauto - Fill in Missing Species Traits Using a Phylogenetic Tree

Imputes missing species trait data for comparative analyses by combining three sources of information: phylogenetic similarity (closely related species share similar traits), cross-trait correlations (observed traits inform missing ones), and optional environmental covariates (climate, habitat, geography). Handles continuous measurements, counts, binary variables, ordered categories, unordered categories, bounded proportions, zero-inflated counts, and compositional multi-proportion data in a single call. The method blends a phylogenetic baseline with a graph neural network correction; a per-trait gate calibrated on held-out data ensures the network only contributes when it improves on the baseline. Provides conformal prediction intervals (95% coverage) for continuous, count, and ordinal traits and supports Rubin's-rules multiple imputation for downstream inference, including tree-uncertainty propagation via posterior tree samples. Tested up to 10,000 species. Bundled datasets include a 300-species and a 9,993-species AVONET bird trait + BirdTree phylogeny subset.