pigauto

0.10.0

Fill in Missing Species Traits Using a Phylogenetic Tree

0packages depend

15downloads / year

41.8%test coverage

10/11checks pass

Overview

About

Maintained by Shinichi NakagawaFirst published 2026-07-301 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)

install.packages("pigauto", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("itchyshin/pigauto")

Development version from itchyshin/pigauto. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-pigauto

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-pigauto

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

1NOTE10OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 6.9 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.66

41.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
9 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-31
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,062 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 39%
Documented parameters: 99%
Return-value docs: 100%
References docs: 10%

Downloads

CRAN downloads in the past year

Rank #24,677 · ~0/day · ~1/mo

Releases R versions

Daily download trend is not available in this view yet.

1530 days

1590 days

151 year

Compare downloads with other packages →

Also on3 r2u

Repository

GitHub ↗ itchyshin/pigauto

3Stars

0Forks

1Open issues

0Open PRs

6Releases

655Commits

2Contributors

655 commits · Last activity 2026-07-31

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/itchyshin/pigauto on 2026-08-02.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

data-raw/Dev Container

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-04-06

claude

Most recent: claude on 2026-04-06

Evidence

claude: on 2026-04-06 · evidence B, D
agents-md: on 2026-05-12 · evidence D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (10)

torch ape ggplot2MatrixrlangstatsutilsgraphicsgrDeviceswithr

LinkingTo (0)

none

Suggests (18)

testthat jsonlite knitr rmarkdown pkgdown RSpectra Rphylopars jomo MCMCglmm glmmTMB lme4nlmephangorn phylolm rgbif smcfcs terra phytools

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Shinichi Nakagawa

Author, Maintainer, Copyright holder

Authors (1)

Shinichi Nakagawa

Author, Maintainer, Copyright holder

Shinichi Nakagawa

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

0.10.0Latest
2026-07-30 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-30
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Bundled data: 2.2 MB / 6 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →