Package: pigauto
Title: Fill in Missing Species Traits Using a Phylogenetic Tree
Version: 0.11.1
Authors@R: 
    c(person("Shinichi", "Nakagawa", role = c("aut", "cre", "cph"), email = "itchyshin@gmail.com"),
      person("Daniel", "Noble", role = "ctb"))
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 default
    method is a phylogenetic baseline calibrated on held-out data; an
    optional graph neural network prediction is blended in through a
    per-trait gate that retains a baseline fallback. Covariates can inform
    the network and selected baseline paths. Provides conformal
    prediction intervals for continuous, count, ordinal, and proportion
    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.
    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, covr, yaml, jsonlite, knitr, rmarkdown, pkgdown,
        RSpectra, Rphylopars, jomo, MCMCglmm, brms, glmmTMB, lme4,
        nlme, phangorn, phylolm, rgbif, smcfcs, terra, phytools
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-11-08 17:39:25 UTC; z3437171
Author: Shinichi Nakagawa [aut, cre, cph],
  Daniel Noble [ctb]
Maintainer: Shinichi Nakagawa <itchyshin@gmail.com>
Repository: CRAN
Date/Publication: 2026-11-09 13:20:02 UTC
