{
  "_id": "6a1f0668b401979e7341bbca",
  "Package": "cauphy",
  "Version": "1.0.3",
  "Title": "Trait Evolution on Phylogenies Using the Cauchy Process",
  "Description": "The Cauchy Process can model pulsed continuous trait\nevolution on phylogenies. The likelihood is tractable, and is\nused for parameter inference and ancestral trait\nreconstruction. See Bastide and Didier (2023)\n<doi:10.1093/sysbio/syad053>.",
  "Authors@R": "c(\nperson(\"Gilles\", \"Didier\", email = \"gilles.didier@free.fr\", role = c(\"aut\", \"cph\")),\nperson(\"Paul\", \"Bastide\", email = \"paul.bastide@cnrs.fr\", role = c(\"aut\", \"cre\")))",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "URL": "https://gilles-didier.github.io/cauphy/",
  "BugReports": "https://github.com/gilles-didier/cauphy/issues",
  "Language": "en-US",
  "Config/pak/sysreqs": "cmake",
  "Repository": "https://gilles-didier.r-universe.dev",
  "Date/Publication": "2024-10-01 17:01:34 UTC",
  "RemoteUrl": "https://github.com/gilles-didier/cauphy",
  "RemoteRef": "HEAD",
  "RemoteSha": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-18 07:04:15 UTC",
    "User": "root"
  },
  "Author": "Gilles Didier [aut, cph],\nPaul Bastide [aut, cre]",
  "Maintainer": "Paul Bastide <paul.bastide@cnrs.fr>",
  "MD5sum": "4cc040089f0ec66d567923bf678a2882",
  "_user": "gilles-didier",
  "_type": "src",
  "_file": "cauphy_1.0.3.tar.gz",
  "_fileid": "998cd130c5784938aca4d1396516712326f4e8e340c060c3ca3527cd4cd59f67",
  "_filesize": 773372,
  "_sha256": "998cd130c5784938aca4d1396516712326f4e8e340c060c3ca3527cd4cd59f67",
  "_created": "2026-05-18T07:04:15.000Z",
  "_published": "2026-06-02T16:35:52.493Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79121914724,
      "time": 174,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051466520"
    },
    {
      "job": 79121914577,
      "time": 200,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051473396"
    },
    {
      "job": 79121915304,
      "time": 219,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051478245"
    },
    {
      "job": 79121915295,
      "time": 189,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051470860"
    },
    {
      "job": 79121915259,
      "time": 212,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051485340"
    },
    {
      "job": 79121914729,
      "time": 373,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051517179"
    },
    {
      "job": 79121914672,
      "time": 184,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051471177"
    },
    {
      "job": 79121914880,
      "time": 379,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051520068"
    },
    {
      "job": 79121914601,
      "time": 240,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051420546"
    },
    {
      "job": 79121913958,
      "time": 125,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7363923162"
    },
    {
      "job": 79121914598,
      "time": 188,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7051470512"
    },
    {
      "job": 79121914858,
      "time": 147,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7051459823"
    },
    {
      "job": 79121915006,
      "time": 192,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7051471326"
    }
  ],
  "_buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/gilles-didier/cauphy",
  "_commit": {
    "id": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
    "author": "Paul Bastide <paul.bastide@m4x.org>",
    "committer": "Paul Bastide <paul.bastide@m4x.org>",
    "message": "Merge branch 'dev'\n",
    "time": 1727802094
  },
  "_maintainer": {
    "name": "Paul Bastide",
    "email": "paul.bastide@cnrs.fr",
    "login": "pbastide",
    "description": "",
    "uuid": 9268479
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "ape",
      "version": ">= 5.5",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "robustbase",
      "role": "Imports"
    },
    {
      "package": "phylolm",
      "version": ">= 2.6.5",
      "role": "Imports"
    },
    {
      "package": "nloptr",
      "role": "Imports"
    },
    {
      "package": "pracma",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "HDInterval",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "geiger",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "gilles-didier",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "pbastide",
      "count": 59,
      "uuid": 9268479
    },
    {
      "user": "gilles-didier",
      "count": 11,
      "uuid": 11198924
    }
  ],
  "_userbio": {
    "uuid": 11198924,
    "type": "user",
    "name": "Gilles Didier"
  },
  "_downloads": {
    "count": 216,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cauphy"
  },
  "_devurl": "https://github.com/gilles-didier/cauphy",
  "_pkgdown": "https://gilles-didier.github.io/cauphy/",
  "_searchresults": 4,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/cauphy.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/gilles-didier/cauphy",
  "_realowner": "gilles-didier",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2023-09-12"
    },
    {
      "version": "1.0.1",
      "date": "2023-09-19"
    },
    {
      "version": "1.0.2",
      "date": "2023-11-29"
    },
    {
      "version": "1.0.3",
      "date": "2024-10-01"
    }
  ],
  "_exports": [
    "ancestral",
    "cauphylm",
    "compute_vcov",
    "fitCauchy",
    "increment",
    "logDensityTipsCauchy",
    "plot_asr",
    "posteriorDensityAncestral",
    "posteriorDensityIncrement",
    "rTraitCauchy"
  ],
  "_datasets": [
    {
      "name": "lizards",
      "title": "Greater Antillean Anolis lizard dataset",
      "object": "lizards",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "ancestral",
      "title": "Posterior density of a node",
      "topics": [
        "ancestral",
        "ancestral.cauphyfit",
        "ancestral.cauphylm"
      ]
    },
    {
      "page": "cauphylm",
      "title": "Phylogenetic Regression using a Cauchy Process",
      "topics": [
        "cauphylm"
      ]
    },
    {
      "page": "compute_vcov",
      "title": "Compute Approximated Variance Covariance Matrix",
      "topics": [
        "compute_vcov"
      ]
    },
    {
      "page": "fitCauchy",
      "title": "Model fitting for a Cauchy Process",
      "topics": [
        "fitCauchy"
      ]
    },
    {
      "page": "hdi.ancestralCauchy",
      "title": "Highest (Posterior) Density Interval",
      "topics": [
        "hdi.ancestralCauchy"
      ]
    },
    {
      "page": "increment",
      "title": "Posterior density of an increment",
      "topics": [
        "increment",
        "increment.cauphyfit",
        "increment.cauphylm"
      ]
    },
    {
      "page": "lizards",
      "title": "Greater Antillean Anolis lizard dataset",
      "topics": [
        "lizards"
      ]
    },
    {
      "page": "logDensityTipsCauchy",
      "title": "Log Density of a Cauchy Process",
      "topics": [
        "logDensityTipsCauchy"
      ]
    },
    {
      "page": "plot_asr",
      "title": "Plot Ancestral States Reconstructions",
      "topics": [
        "plot_asr"
      ]
    },
    {
      "page": "plot.ancestralCauchy",
      "title": "Plot for class 'ancestralCauchy'",
      "topics": [
        "plot.ancestralCauchy"
      ]
    },
    {
      "page": "plot.profile.cauphyfit",
      "title": "Plot for class 'profile.cauphyfit'",
      "topics": [
        "plot.profile.cauphyfit"
      ]
    },
    {
      "page": "posteriorDensityAncestral",
      "title": "Posterior density of a node",
      "topics": [
        "posteriorDensityAncestral"
      ]
    },
    {
      "page": "posteriorDensityIncrement",
      "title": "Posterior density of an increment",
      "topics": [
        "posteriorDensityIncrement"
      ]
    },
    {
      "page": "vcov.cauphyfit",
      "title": "Generic Methods for S3 class 'cauphyfit'.",
      "topics": [
        "AIC.cauphyfit",
        "AIC.logLik.cauphyfit",
        "coef.cauphyfit",
        "confint.cauphyfit",
        "logLik.cauphyfit",
        "print.cauphyfit",
        "vcov.cauphyfit"
      ]
    },
    {
      "page": "vcov.cauphylm",
      "title": "Generic Methods for S3 class 'cauphylm'.",
      "topics": [
        "AIC.cauphylm",
        "AIC.logLik.cauphylm",
        "coef.cauphylm",
        "confint.cauphylm",
        "logLik.cauphylm",
        "predict.cauphylm",
        "print.cauphylm",
        "vcov.cauphylm"
      ]
    },
    {
      "page": "profile.cauphyfit",
      "title": "Method for Profiling 'cauphyfit' Objects",
      "topics": [
        "profile.cauphyfit"
      ]
    },
    {
      "page": "rTraitCauchy",
      "title": "Cauchy Trait Simulation",
      "topics": [
        "rTraitCauchy"
      ]
    }
  ],
  "_readme": "https://github.com/gilles-didier/cauphy/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "codetools",
    "DEoptimR",
    "digest",
    "doParallel",
    "foreach",
    "future",
    "future.apply",
    "globals",
    "HDInterval",
    "iterators",
    "lattice",
    "listenv",
    "nlme",
    "nloptr",
    "parallelly",
    "phylolm",
    "pracma",
    "Rcpp",
    "robustbase"
  ],
  "_vignettes": [
    {
      "source": "lizards.Rmd",
      "filename": "lizards.html",
      "title": "Example Analysis",
      "author": "Paul Bastide",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Dataset",
        "Cauchy Process Fit - REML",
        "Cauchy Process Fit - ML",
        "Model Selection",
        "Ancestral Trait Reconstruction",
        "Ancestral Branch Increment Reconstruction",
        "Schematic Plot of Ancestral Reconstructions"
      ],
      "created": "2023-03-22 14:35:01",
      "modified": "2023-09-11 16:16:33",
      "commits": 5
    }
  ],
  "_score": 3.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "cauphy",
  "_universes": [
    "gilles-didier",
    "pbastide"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-05-18T07:06:40.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "97e1f9929483b248aba75f626bb59b714e85f78ea8c5eca9f8971d6ebd6af71a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-05-18T07:06:53.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "a3e197233fa077e28725862ab9cb0343b6f7b558c2facc0cca1b963cc7783c06",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-05-18T07:07:27.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "8159e0eea8f7db251a6ef1e85b2bd2a2dfbab3c370d81483936e731b1ae3fbe5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.3",
      "date": "2026-05-18T07:06:44.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "ef0be8045a1e19c4b4f10bfd28ffbd866d8c2fe39785e5c57f54bf46ea0c7855",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-05-18T07:07:55.000Z",
      "arch": "aarch64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "f645543bd57705f6d49e9d5941b2e982635256290e1803a05a3cb515399d8521",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-05-18T07:09:07.000Z",
      "arch": "x86_64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "bd8178e363482728fd57177cb79d0238c035b670f5d3ef669cb5f40b24bd7b48",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-05-18T07:07:01.000Z",
      "arch": "aarch64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "e37402bd9efb933ae9fc3b8d61def33370a24157e77a02f58aaaa4c72f827598",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.3",
      "date": "2026-05-18T07:08:54.000Z",
      "arch": "x86_64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "3841d6f5dd6e4e7d7764a103107e294953783e351ab7aaf75ff6598f56e7cd0d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-05-18T07:06:15.000Z",
      "arch": "x86_64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "a3e617af5228d5b228cb278a0cdf50586843be61430c563f08c8d0d9d84f1d36",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-05-18T07:05:39.000Z",
      "arch": "x86_64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "60a8f6ebd1af166ac287367c4d78fbfd8b975e44acd3c979ee9a1d98970ee671",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.3",
      "date": "2026-05-18T07:05:57.000Z",
      "arch": "x86_64",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "9a834847de126eeae7f64a4d6c829429b7309e6bc6d2f59581794f4203827639",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.3",
      "date": "2026-06-02T16:35:28.000Z",
      "arch": "emscripten",
      "commit": "5d65b3d1b456d61810f2c78442cddf4a8de1aa8a",
      "fileid": "c2eaf373cfbe1cc3e6c4c86b0a75016a6da80e30a071ddd585fb6a3c61a3985b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/gilles-didier/actions/runs/26018504278"
    }
  ]
}