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
• Package README

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