Package: pigauto
Title: Fill in Missing Species Traits Using a Phylogenetic Tree
Version: 0.10.0
Authors@R: 
    person("Shinichi", "Nakagawa", role = c("aut", "cre", "cph"), email = "itchyshin@gmail.com")
Description: 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>.
License: MIT + file LICENSE
URL: https://itchyshin.github.io/pigauto/,
        https://github.com/itchyshin/pigauto
BugReports: https://github.com/itchyshin/pigauto/issues
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
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
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Repository: https://itchyshin.r-universe.dev
Date/Publication: 2026-07-21 17:23:10 UTC
RemoteUrl: https://github.com/itchyshin/pigauto
RemoteRef: main
RemoteSha: 0cc11c5a0d9dd0ecc4862d890f35318bef29c8d8
NeedsCompilation: no
Packaged: 2026-07-21 18:05:12 UTC; root
Author: Shinichi Nakagawa [aut, cre, cph]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>