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 for continuous, count, and ordinal traits and an experimental analysis-aware multiple-imputation workflow for one missing continuous covariate in Gaussian linear, binomial-logit, and Gaussian random-intercept models, with Rubin pooling limited to fixed effects. Stochastic graph-network and posterior-tree completions are prediction diagnostics rather than validated inferential imputations. Tested up to 10,000 species. Bundled datasets include 300-species and 9,993-species bird-trait subsets with matching example phylogenetic trees. Rubin (1987, ISBN:978-0-471-08705-2); Vovk et al. (2005, ISBN:978-0-387-25061-8); Nakagawa and de Villemereuil (2019) <doi:10.1093/sysbio/syy089>.
| Version: | 0.10.0 |
| Depends: | R (≥ 4.1) |
| Imports: | torch, ape, ggplot2, Matrix, rlang, stats, utils, graphics, grDevices, withr |
| Suggests: | testthat, jsonlite, knitr, rmarkdown, pkgdown, RSpectra, Rphylopars, jomo, MCMCglmm, glmmTMB, lme4, nlme, phangorn, phylolm, rgbif, smcfcs, terra, phytools |
| Published: | 2026-07-30 |
| DOI: | 10.32614/CRAN.package.pigauto (may not be active yet) |
| Author: | Shinichi Nakagawa [aut, cre, cph] |
| Maintainer: | Shinichi Nakagawa <itchyshin at gmail.com> |
| BugReports: | https://github.com/itchyshin/pigauto/issues |
| License: | MIT + file LICENSE |
| URL: | https://itchyshin.github.io/pigauto/, https://github.com/itchyshin/pigauto |
| NeedsCompilation: | no |
| Materials: | README, NEWS |
| CRAN checks: | pigauto results |
| Reference manual: | pigauto.html , pigauto.pdf |
| Vignettes: |
Common pitfalls / FAQ (source, R code) Getting started with pigauto (source, R code) GNN architecture and the math behind pigauto (source, R code) Mixed-Type Trait Imputation (source, R code) Posterior-Tree Prediction Sensitivity (source, R code) |
| Package source: | pigauto_0.10.0.tar.gz |
| Windows binaries: | r-devel: pigauto_0.10.0.zip, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): pigauto_0.10.0.tgz, r-oldrel (arm64): pigauto_0.10.0.tgz, r-release (x86_64): pigauto_0.10.0.tgz, r-oldrel (x86_64): pigauto_0.10.0.tgz |
Please use the canonical form https://CRAN.R-project.org/package=pigauto to link to this page.