{ "_id": "6ad80fa1d556c3a3418a7d59", "Package": "pigauto", "Title": "Fill in Missing Species Traits Using a Phylogenetic Tree", "Version": "0.11.0", "Authors@R": "person(\"Shinichi\", \"Nakagawa\", role = c(\"aut\", \"cre\", \"cph\"), email = \"itchyshin@gmail.com\")", "Description": "Imputes missing species trait data for comparative\nanalyses by combining three sources of information:\nphylogenetic similarity (closely related species share similar\ntraits), cross-trait correlations (observed traits inform\nmissing ones), and optional environmental covariates (climate,\nhabitat, geography). Handles continuous measurements, counts,\nbinary variables, ordered categories, unordered categories,\nbounded proportions, zero-inflated counts, and compositional\nmulti-proportion data in a single call. The default method is a\nphylogenetic baseline calibrated on held-out data; an optional\ngraph neural network correction, which is needed to use\ncovariates, is blended in through a per-trait gate that retains\na baseline fallback. Provides conformal prediction intervals\nfor continuous, count, ordinal, and proportion traits and an\nexperimental analysis-aware multiple-imputation workflow for\none missing continuous covariate in Gaussian linear,\nbinomial-logit, and Gaussian random-intercept models, with\nRubin pooling limited to fixed effects. Stochastic\ngraph-network and posterior-tree completions are prediction\ndiagnostics rather than validated inferential imputations.\nBundled datasets include 300-species and 9,993-species\nbird-trait subsets with matching example phylogenetic trees.\nRubin (1987, ISBN:978-0-471-08705-2); Vovk et al. (2005,\nISBN:978-0-387-25061-8); Nakagawa and de Villemereuil (2019)\n.", "License": "MIT + file LICENSE", "URL": "https://itchyshin.github.io/pigauto/,\nhttps://github.com/itchyshin/pigauto", "BugReports": "https://github.com/itchyshin/pigauto/issues", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Repository": "https://itchyshin.r-universe.dev", "Date/Publication": "2026-10-20 22:40:09 UTC", "RemoteUrl": "https://github.com/itchyshin/pigauto", "RemoteRef": "main", "RemoteSha": "a44e76e67f6b8951771c7fdca1ac13769df04c2c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-21 00:54:08 UTC", "User": "root" }, "Author": "Shinichi Nakagawa [aut, cre, cph]", "Maintainer": "Shinichi Nakagawa ", "_user": "itchyshin", "_type": "src", "_file": "pigauto_0.11.0.tar.gz", "_fileid": "https://r2.ropensci.org/c095c568d1ad7b2a7b9e839125f8fa287d7e4d6ae41434669efeb88917c43087", "_filesize": 5779980, "_sha256": "c095c568d1ad7b2a7b9e839125f8fa287d7e4d6ae41434669efeb88917c43087", "_expires": "2027-01-29T01:04:31.000Z", "_created": "2026-10-21T00:54:08.000Z", "_published": "2026-10-21T01:04:33.500Z", "_buildurl": "https://github.com/r-universe/itchyshin/actions/runs/39523261314", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 118974818612, "time": 343, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12311609469" }, { "job": 118974818714, "time": 465, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12311654730" }, { "job": 118974818602, "time": 262, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12311534397" }, { "job": 118974818680, "time": 278, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12311329600" }, { "job": 118971978458, "time": 527, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12311829009" }, { "job": 118974818613, "time": 314, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12311999807" }, { "job": 118974818597, "time": 323, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12312354499" }, { "job": 118974818583, "time": 310, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12311814810" }, { "job": 118974818682, "time": 569, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12313755120" } ], "_upstream": "https://github.com/itchyshin/pigauto", "_commit": { "id": "a44e76e67f6b8951771c7fdca1ac13769df04c2c", "author": "Shinichi Nakagawa ", "committer": "GitHub ", "message": "Merge pull request #247 from itchyshin/codex/gnn-pagefix-closeout-20261020\n\ndocs: record GNN page-fix closeout", "time": 1792536009 }, "_maintainer": { "name": "Shinichi Nakagawa", "email": "itchyshin@gmail.com", "login": "itchyshin", "description": "An evolutionary biologist (with some Darwinian fitness in his arms), trying to learn how to use Git and R together. 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