{
  "_id": "6ad1f4d51200a49930211b71",
  "Package": "BMhyb",
  "Version": "2.1.5",
  "Date": "2019-08-02",
  "Type": "Package",
  "Title": "Comparative Methods for Phylogenetic Networks",
  "Authors@R": "c(person(\"Dwueng-Chwuan\", \"Jhwueng\", role = c(\"aut\", \"cre\"),\nemail = \"djhwueng@umail.iu.edu\"),\nperson(\"Brian C.\", \"O'Meara\", role = c(\"aut\"),\nemail = \"omeara.brian@gmail.com\"))",
  "Description": "Analyze the phenotypic evolution of species of hybrid\norigin on a phylogenetic network. This can detect a burst of\nvariation at the formation of a hybrid as well as an increase\nor decrease in trait value at a hybridization event. Parameters\nare estimated by maximum likelihood, and model averaging can be\ndone automatically. Users need to enter a comparative data set\nand a phylogenetic network.",
  "License": "GPL (>=2)",
  "URL": "http://github.com/bomeara/BMhyb",
  "BugReports": "https://github.com/bomeara/BMhyb/issues",
  "RoxygenNote": "7.1.1",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libicu-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev",
  "Repository": "https://bomeara.r-universe.dev",
  "Date/Publication": "2021-11-08 16:09:12 UTC",
  "RemoteUrl": "https://github.com/bomeara/BMhyb",
  "RemoteRef": "HEAD",
  "RemoteSha": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-16 09:44:35 UTC",
    "User": "root"
  },
  "Author": "Dwueng-Chwuan Jhwueng [aut, cre],\nBrian C. O'Meara [aut]",
  "Maintainer": "Dwueng-Chwuan Jhwueng <djhwueng@umail.iu.edu>",
  "_user": "bomeara",
  "_type": "src",
  "_file": "BMhyb_2.1.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/814a6185ea3d7614f9d35ba19b3771fbe546360ab699f71c83d6e6a3d66d93ad",
  "_filesize": 193630,
  "_sha256": "814a6185ea3d7614f9d35ba19b3771fbe546360ab699f71c83d6e6a3d66d93ad",
  "_expires": "2027-01-24T09:56:36.000Z",
  "_created": "2026-10-16T09:44:35.000Z",
  "_published": "2026-10-16T09:56:37.686Z",
  "_buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 116912543945,
      "time": 190,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12037638735"
    },
    {
      "job": 116912544035,
      "time": 268,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12038432379"
    },
    {
      "job": 116912543969,
      "time": 169,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12038453464"
    },
    {
      "job": 116912543992,
      "time": 172,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12039175511"
    },
    {
      "job": 116911006572,
      "time": 246,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12037199530"
    },
    {
      "job": 116912544020,
      "time": 136,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12038475908"
    },
    {
      "job": 116912543919,
      "time": 273,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "12037689883"
    },
    {
      "job": 116912544067,
      "time": 170,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "12037549004"
    },
    {
      "job": 116912544102,
      "time": 302,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "12038490819"
    }
  ],
  "_upstream": "https://github.com/bomeara/BMhyb",
  "_commit": {
    "id": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
    "author": "Brian O'Meara <omeara.brian@gmail.com>",
    "committer": "Brian O'Meara <omeara.brian@gmail.com>",
    "message": "updating to fix failed git issue\n",
    "time": 1636387752
  },
  "_maintainer": {
    "name": "Dwueng-Chwuan Jhwueng",
    "email": "djhwueng@umail.iu.edu"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "corpcor",
      "role": "Imports"
    },
    {
      "package": "numDeriv",
      "role": "Imports"
    },
    {
      "package": "geiger",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "TreeSim",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "lhs",
      "role": "Imports"
    },
    {
      "package": "viridis",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "DEoptim",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "metR",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bomeara",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "bomeara",
      "count": 265,
      "uuid": 1612612
    }
  ],
  "_userbio": {
    "uuid": 1612612,
    "type": "user",
    "name": "Brian O'Meara",
    "followers": 112
  },
  "_downloads": {
    "count": 30,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BMhyb"
  },
  "_devurl": "https://github.com/bomeara/bmhyb",
  "_searchresults": 137,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/BMhyb.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.5.1",
      "date": "2017-09-11"
    },
    {
      "version": "1.5.2",
      "date": "2017-10-08"
    },
    {
      "version": "2.1.5",
      "date": "2019-08-02"
    }
  ],
  "_exports": [
    "AddHybridization",
    "BMhyb",
    "BMhybExhaustive",
    "ComputeLikelihood",
    "ComputeVCV",
    "ConvertEvonetToIgraphWithNodeNumbers",
    "CreateHybridlessEvonet",
    "MergeExhaustiveForPlotting",
    "SimulateNetwork",
    "SimulateTips"
  ],
  "_datasets": [
    {
      "name": "cichlid",
      "title": "Cichlid dataset",
      "object": "cichlid",
      "file": "cichlid.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "nicotiana",
      "title": "Nicotiana dataset",
      "object": "nicotiana",
      "file": "nicotiana.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "AddHybridization",
      "title": "Add hybrid events to a phy.graph",
      "topics": [
        "AddHybridization"
      ]
    },
    {
      "page": "BMhyb",
      "title": "Optimize model",
      "topics": [
        "BMhyb"
      ]
    },
    {
      "page": "BMhybExhaustive",
      "title": "Exhaustively evaluate models",
      "topics": [
        "BMhybExhaustive"
      ]
    },
    {
      "page": "cichlid",
      "title": "Cichlid dataset",
      "topics": [
        "cichlid"
      ]
    },
    {
      "page": "ComputeLikelihood",
      "title": "Compute the likelihood for a set of parameters",
      "topics": [
        "ComputeLikelihood"
      ]
    },
    {
      "page": "ComputeVCV",
      "title": "Compute the variance-covariance matrix",
      "topics": [
        "ComputeVCV"
      ]
    },
    {
      "page": "ConvertEvonetToIgraphWithNodeNumbers",
      "title": "Convert an evonet object into igraph",
      "topics": [
        "ConvertEvonetToIgraphWithNodeNumbers"
      ]
    },
    {
      "page": "CreateHybridlessEvonet",
      "title": "Convert phylo object to evonet",
      "topics": [
        "CreateHybridlessEvonet"
      ]
    },
    {
      "page": "GetConvexHull",
      "title": "Get convex hull at a given threshold",
      "topics": [
        "GetConvexHull"
      ]
    },
    {
      "page": "MergeExhaustiveForPlotting",
      "title": "Function to merge adaptive sampling sims for plotting",
      "topics": [
        "MergeExhaustiveForPlotting"
      ]
    },
    {
      "page": "nicotiana",
      "title": "Nicotiana dataset",
      "topics": [
        "nicotiana"
      ]
    },
    {
      "page": "plot.BMhybExhaustiveResult",
      "title": "Plot BMhybExhaustive result",
      "topics": [
        "plot.BMhybExhaustiveResult"
      ]
    },
    {
      "page": "plot.BMhybResult",
      "title": "Plot BMhyb result",
      "topics": [
        "plot.BMhybResult"
      ]
    },
    {
      "page": "print.BMhybExhaustiveResult",
      "title": "Print BMhybExhaustive result",
      "topics": [
        "print.BMhybExhaustiveResult"
      ]
    },
    {
      "page": "print.BMhybResult",
      "title": "Print BMhyb result",
      "topics": [
        "print.BMhybResult"
      ]
    },
    {
      "page": "SimulateNetwork",
      "title": "Simulate a phylogenetic network",
      "topics": [
        "SimulateNetwork"
      ]
    },
    {
      "page": "SimulateTips",
      "title": "Simulate trait data",
      "topics": [
        "SimulateTips"
      ]
    },
    {
      "page": "summary.BMhybExhaustiveResult",
      "title": "Summarize BMhybExhaustive result",
      "topics": [
        "summary.BMhybExhaustiveResult"
      ]
    },
    {
      "page": "summary.BMhybResult",
      "title": "Summarize BMhyb result",
      "topics": [
        "summary.BMhybResult"
      ]
    }
  ],
  "_readme": "https://github.com/bomeara/BMhyb/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "backports",
    "cachem",
    "checkmate",
    "class",
    "classInt",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "colorspace",
    "combinat",
    "corpcor",
    "cowplot",
    "cpp11",
    "data.table",
    "DBI",
    "DEoptim",
    "deSolve",
    "digest",
    "doParallel",
    "e1071",
    "expm",
    "farver",
    "fastmap",
    "fastmatch",
    "foreach",
    "Formula",
    "formula.tools",
    "geiger",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "igraph",
    "isoband",
    "iterators",
    "KernSmooth",
    "labeling",
    "lattice",
    "lhs",
    "lifecycle",
    "lubridate",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "memoise",
    "metR",
    "mnormt",
    "mvtnorm",
    "ncbit",
    "nlme",
    "numDeriv",
    "operator.tools",
    "optimParallel",
    "phangorn",
    "phytools",
    "pkgconfig",
    "plyr",
    "proxy",
    "purrr",
    "quadprog",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "s2",
    "S7",
    "scales",
    "scatterplot3d",
    "sf",
    "stringi",
    "stringr",
    "subplex",
    "timechange",
    "TreeSim",
    "units",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "wk"
  ],
  "_score": 2.8356905714924254,
  "_indexed": true,
  "_nocasepkg": "bmhyb",
  "_universes": [
    "bomeara"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1.5",
      "date": "2026-10-16T09:46:39.000Z",
      "distro": "resolute",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/18b6a5c23ad2c8dd91a2bbda042a23130eb7f8cbaaa2fa324e6aa7b2c909b9d1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.1.5",
      "date": "2026-10-16T09:46:50.000Z",
      "distro": "resolute",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/53f174710bf5f73199663c703deb61d278cd83ce2627fe4c82a6300a08ccdffb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1.5",
      "date": "2026-10-16T09:54:38.000Z",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/da754dd9cc5b6c7e15e20ced9d6b31928cced9cae6f8a44c58672bf3f38bcd26",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.1.5",
      "date": "2026-10-16T09:54:50.000Z",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/c85d811736cdb523d941606c20912a1afd13337b9c31517fca1420884569a2a9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1.5",
      "date": "2026-10-16T09:47:01.000Z",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/210c37489f658ff6d58a062d849633c0dcf8c25fd72de17804a9312aa66ea71d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1.5",
      "date": "2026-10-16T09:45:40.000Z",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/1424102db579ad8485747a8aab57b112e4b836d83c22cb3fb227c4e7fce801d2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1.5",
      "date": "2026-10-16T09:45:54.000Z",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/eacf9b5c43be9283a39dca1bfae16d912b9dda1cd1d40558f1c8143e1ad3148b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.1.5",
      "date": "2026-10-16T09:45:48.000Z",
      "commit": "22709ce2792695c1bf34e1a4a224c973eeb889e8",
      "fileid": "https://r2.ropensci.org/679609b5609994611a5ffc2b6971ebc5c68908f7a50b6858cde48242b63dd87f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38882050862"
    }
  ]
}