{
  "_id": "6a1ed4e1b401979e7340e3d8",
  "Package": "Rphylopars",
  "Version": "0.3.9",
  "Title": "Phylogenetic Comparative Tools for Missing Data and\nWithin-Species Variation",
  "Authors@R": "c(person(\"Eric W.\", \"Goolsby\", role = c(\"aut\", \"cre\"),\nemail = \"eric.goolsby.evolution@gmail.com\"),\nperson(\"Jorn\", \"Bruggeman\", role = \"aut\"),\nperson(\"Cecile\", \"Ane\", role = \"aut\"))",
  "Description": "Tools for performing phylogenetic comparative methods for\ndatasets with with multiple observations per species\n(intraspecific variation or measurement error) and/or missing\ndata (Goolsby et al. 2017). Performs ancestral state\nreconstruction and missing data imputation on the estimated\nevolutionary model, which can be specified as Brownian Motion,\nOrnstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or\ndelta, or a star phylogeny.",
  "Date": "2022-05-08",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/ericgoolsby/Rphylopars/wiki",
  "RoxygenNote": "7.1.1",
  "NeedsCompilation": "yes",
  "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev",
  "Repository": "https://ericgoolsby.r-universe.dev",
  "Date/Publication": "2022-05-09 14:13:43 UTC",
  "RemoteUrl": "https://github.com/ericgoolsby/rphylopars",
  "RemoteRef": "HEAD",
  "RemoteSha": "284efae471cafa1ed3a87268cbe589078ce20708",
  "Packaged": {
    "Date": "2026-05-20 10:39:47 UTC",
    "User": "root"
  },
  "Author": "Eric W. Goolsby [aut, cre],\nJorn Bruggeman [aut],\nCecile Ane [aut]",
  "Maintainer": "Eric W. Goolsby <eric.goolsby.evolution@gmail.com>",
  "MD5sum": "e64a8ed8f9e7ab65a64037b364fae167",
  "_user": "ericgoolsby",
  "_type": "src",
  "_file": "Rphylopars_0.3.9.tar.gz",
  "_fileid": "ebcd06b849159ea861cce7e695519d2c27f2f01f6c99da2102cb329e9c4bbbdc",
  "_filesize": 170827,
  "_sha256": "ebcd06b849159ea861cce7e695519d2c27f2f01f6c99da2102cb329e9c4bbbdc",
  "_created": "2026-05-20T10:39:47.000Z",
  "_published": "2026-06-02T13:04:33.295Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79076876503,
      "time": 220,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7107827484"
    },
    {
      "job": 79076876532,
      "time": 193,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7107819205"
    },
    {
      "job": 79076877270,
      "time": 183,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7107815891"
    },
    {
      "job": 79076876498,
      "time": 251,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7107837779"
    },
    {
      "job": 79076876850,
      "time": 169,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7108004110"
    },
    {
      "job": 79076876837,
      "time": 262,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7108012867"
    },
    {
      "job": 79076876705,
      "time": 162,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7107998172"
    },
    {
      "job": 79076876645,
      "time": 291,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7108029846"
    },
    {
      "job": 79076876554,
      "time": 247,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7107755063"
    },
    {
      "job": 79076875659,
      "time": 136,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7358442418"
    },
    {
      "job": 79076876562,
      "time": 179,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7107813993"
    },
    {
      "job": 79076876746,
      "time": 277,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7107845910"
    },
    {
      "job": 79076876803,
      "time": 173,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7107812602"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ericgoolsby/rphylopars",
  "_commit": {
    "id": "284efae471cafa1ed3a87268cbe589078ce20708",
    "author": "Eric W. Goolsby <eric.goolsby.evolution@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #53 from ericgoolsby/devel\n\nUpdate README.md",
    "time": 1652105623
  },
  "_maintainer": {
    "name": "Eric W. Goolsby",
    "email": "eric.goolsby.evolution@gmail.com",
    "login": "ericgoolsby",
    "description": "",
    "uuid": 9159588
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "ape",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "doBy",
      "role": "Imports"
    },
    {
      "package": "phylolm",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "numDeriv",
      "role": "Imports"
    }
  ],
  "_owner": "ericgoolsby",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 32,
  "_contributors": [
    {
      "user": "ericgoolsby",
      "count": 84,
      "uuid": 9159588
    },
    {
      "user": "r03ert0",
      "count": 7,
      "uuid": 2310732
    },
    {
      "user": "tdjames1",
      "count": 1,
      "uuid": 10053102
    }
  ],
  "_userbio": {
    "uuid": 9159588,
    "type": "user",
    "name": "Eric W. Goolsby"
  },
  "_downloads": {
    "count": 633,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rphylopars"
  },
  "_mentions": 11,
  "_devurl": "https://github.com/ericgoolsby/rphylopars",
  "_searchresults": 126,
  "_topics": [
    "openblas",
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Rphylopars.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ericgoolsby/rphylopars",
  "_realowner": "ericgoolsby",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2015-06-01"
    },
    {
      "version": "0.1.1",
      "date": "2015-06-02"
    },
    {
      "version": "0.2.1",
      "date": "2016-03-12"
    },
    {
      "version": "0.2.8",
      "date": "2016-06-15"
    },
    {
      "version": "0.2.9",
      "date": "2016-06-16"
    },
    {
      "version": "0.2.11",
      "date": "2019-10-21"
    },
    {
      "version": "0.2.12",
      "date": "2019-12-12"
    },
    {
      "version": "0.3.0",
      "date": "2020-05-14"
    },
    {
      "version": "0.3.2",
      "date": "2021-02-06"
    },
    {
      "version": "0.3.9",
      "date": "2022-05-09"
    },
    {
      "version": "0.3.10",
      "date": "2024-01-19"
    }
  ],
  "_exports": [
    "anc.recon",
    "anova.phylopars.lm",
    "fast.SSC",
    "logLik.phylopars",
    "logLik.phylopars.lm",
    "phylopars",
    "phylopars.lm",
    "print.phylopars",
    "print.phylopars.lm",
    "print.SSC",
    "simtraits",
    "summary.phylopars",
    "summary.phylopars.lm",
    "write.phylopars"
  ],
  "_help": [
    {
      "page": "Rphylopars-package",
      "title": "Phylogenetic Comparative Tools for Missing Data and Within-Species Variation",
      "topics": [
        "Rphylopars-package"
      ]
    },
    {
      "page": "anc.recon",
      "title": "Ultra-fast maximum likelihood ancestral state reconstruction",
      "topics": [
        "anc.recon"
      ]
    },
    {
      "page": "anova.phylopars.lm",
      "title": "Phylopars regression ANOVA",
      "topics": [
        "anova.phylopars.lm"
      ]
    },
    {
      "page": "fast.SSC",
      "title": "Fast Phylogenetic Signal Using Sum of Squared Changes (SSC)",
      "topics": [
        "fast.SSC"
      ]
    },
    {
      "page": "logLik.phylopars",
      "title": "Extract Log_likelihood",
      "topics": [
        "logLik.phylopars"
      ]
    },
    {
      "page": "logLik.phylopars.lm",
      "title": "Extract Log_likelihood",
      "topics": [
        "logLik.phylopars.lm"
      ]
    },
    {
      "page": "phylopars",
      "title": "Estimation of phylogenetic and phenotypic covariance parameters",
      "topics": [
        "phylopars"
      ]
    },
    {
      "page": "phylopars.lm",
      "title": "Rphylopars regression",
      "topics": [
        "phylopars.lm"
      ]
    },
    {
      "page": "print.phylopars",
      "title": "Print phylopars",
      "topics": [
        "print.phylopars"
      ]
    },
    {
      "page": "print.phylopars.lm",
      "title": "Print phylopars.lm",
      "topics": [
        "print.phylopars.lm"
      ]
    },
    {
      "page": "print.SSC",
      "title": "Print SSC",
      "topics": [
        "print.SSC"
      ]
    },
    {
      "page": "simtraits",
      "title": "Simulate traits for phylopars estimation",
      "topics": [
        "simtraits"
      ]
    },
    {
      "page": "summary.phylopars",
      "title": "Phylopars summary",
      "topics": [
        "summary.phylopars"
      ]
    },
    {
      "page": "summary.phylopars.lm",
      "title": "phylopars.lm summary",
      "topics": [
        "summary.phylopars.lm"
      ]
    },
    {
      "page": "write.phylopars",
      "title": "Write data and tree files for Python phylopars compatability.",
      "topics": [
        "write.phylopars"
      ]
    }
  ],
  "_readme": "https://github.com/ericgoolsby/rphylopars/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "backports",
    "boot",
    "broom",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "colorspace",
    "combinat",
    "cowplot",
    "cpp11",
    "DEoptim",
    "Deriv",
    "digest",
    "doBy",
    "doParallel",
    "dplyr",
    "expm",
    "farver",
    "fastmatch",
    "foreach",
    "forecast",
    "fracdiff",
    "future",
    "future.apply",
    "generics",
    "ggplot2",
    "globals",
    "glue",
    "gtable",
    "igraph",
    "isoband",
    "iterators",
    "labeling",
    "lattice",
    "lifecycle",
    "listenv",
    "lmtest",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "microbenchmark",
    "mnormt",
    "modelr",
    "nlme",
    "nnet",
    "numDeriv",
    "optimParallel",
    "parallelly",
    "phangorn",
    "phylolm",
    "phytools",
    "pillar",
    "pkgconfig",
    "purrr",
    "quadprog",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S7",
    "scales",
    "scatterplot3d",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 7.082641778157132,
  "_indexed": true,
  "_nocasepkg": "rphylopars",
  "_universes": [
    "ericgoolsby"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.9",
      "date": "2026-05-20T10:43:03.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "65505e4994392f88eb3e6b727a53b170abe7ce57024afa8d7fac170a79fc744d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.9",
      "date": "2026-05-20T10:42:31.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "a5384d8a77adb250f09cae55e6e62b0b4c420e7c56e47636e461f4fd94402ce1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.9",
      "date": "2026-05-20T10:42:29.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "18721cffe7d3c89ba89d1861bfcc1bd4b8f87c24d0af29710ce833a2558ede83",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.9",
      "date": "2026-05-20T10:43:27.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "f63bd11aee6befca26cf2ad669586ee879cf09ed99ddaf5b84e2e1a61dc28428",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.9",
      "date": "2026-05-20T10:52:06.000Z",
      "arch": "aarch64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "b38b8d22600f18fd523a4090ef9b2cb5d6d9a787ebda298bafb5a5470338002e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.9",
      "date": "2026-05-20T10:51:58.000Z",
      "arch": "x86_64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "a4885adc43aafe605093021cc43489e42b34a8b3e46bf5a206c0dd322e00e25e",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.3.9",
      "date": "2026-05-20T10:51:52.000Z",
      "arch": "aarch64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "711946e0a7815fa697aaa40190f5fc7be9b6ff8f27f2be1f43a9a9c30eb84066",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.3.9",
      "date": "2026-05-20T10:52:47.000Z",
      "arch": "x86_64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "9f783e4fb58951d4b737a35dbfb9b248cc809a5347f232cf7a35b8abf3603fa0",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.3.9",
      "date": "2026-05-20T10:41:38.000Z",
      "arch": "x86_64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "b8f4d7d9630c2786b51780f0c4da6089d4fd6ba50cc772e6a60cfa1832d34ec8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.3.9",
      "date": "2026-05-20T10:41:53.000Z",
      "arch": "x86_64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "30a7b445905fc0780c2f973c35f54e2551928e80012b61afe4a79d9577efe988",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.3.9",
      "date": "2026-05-20T10:41:30.000Z",
      "arch": "x86_64",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "ccd3676a988e2fe6dfc7f6fcb5e2b567589e5fe65896621500a4008ed6fa1558",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.3.9",
      "date": "2026-06-02T13:03:51.000Z",
      "arch": "emscripten",
      "commit": "284efae471cafa1ed3a87268cbe589078ce20708",
      "fileid": "ff106456e2082a84bd36a184ba08afaf5d7db99f7e794150b0e01f81c7ac5d62",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ericgoolsby/actions/runs/26157086118"
    }
  ]
}