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
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-07-21 17:17:26 UTC; z3437171
Author: Shinichi Nakagawa [aut, cre, cph]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Repository: CRAN
Date/Publication: 2026-07-30 17:10:22 UTC
Built: R 4.7.0; ; 2026-08-11 04:04:16 UTC; windows
