{
  "_id": "6a10369facfb0bcc41c9a0d5",
  "Package": "TreeSim",
  "Type": "Package",
  "Title": "Simulating Phylogenetic Trees",
  "Version": "2.4",
  "Date": "2019-03-08",
  "Author": "Tanja Stadler",
  "Maintainer": "Tanja Stadler <tanja.stadler@bsse.ethz.ch>",
  "Description": "Simulation methods for phylogenetic trees where (i) all\ntips are sampled at one time point or (ii) tips are sampled\nsequentially through time. (i) For sampling at one time point,\nsimulations are performed under a constant rate birth-death\nprocess, conditioned on having a fixed number of final tips\n(sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age\nand number of tips (sim.bd.taxa.age()). When conditioning on\nthe number of final tips, the method allows for shifts in rates\nand mass extinction events during the birth-death process\n(sim.rateshift.taxa()). The function sim.bd.age() (and\nsim.rateshift.taxa() without extinction) allow the speciation\nrate to change in a density-dependent way. The LTT plots of the\nsimulations can be displayed using LTT.plot(), LTT.plot.gen()\nand LTT.average.root(). TreeSim further samples trees with n\nfinal tips from a set of trees generated by the common sampling\nalgorithm stopping when a fixed number m>>n of tips is first\nreached (sim.gsa.taxa()). This latter method is appropriate for\nm-tip trees generated under a big class of models (details in\nthe sim.gsa.taxa() man page). For incomplete phylogeny, the\nmissing speciation events can be added through simulations\n(corsim()). (ii) sim.rateshifts.taxa() is generalized to\nsim.bdsky.stt() for serially sampled trees, where the trees are\nconditioned on either the number of sampled tips or the age.\nFurthermore, for a multitype-branching process with sequential\nsampling, trees on a fixed number of tips can be simulated\nusing sim.bdtypes.stt.taxa(). This function further allows to\nsimulate under epidemiological models with an exposed class.\nThe function sim.genespeciestree() simulates coalescent gene\ntrees within birth-death species trees, and sim.genetree()\nsimulates coalescent gene trees.",
  "License": "GPL-2",
  "LazyLoad": "yes",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-12 06:42:05 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://tanja819.r-universe.dev",
  "Date/Publication": "2019-04-08 15:52:56 UTC",
  "RemoteUrl": "https://github.com/cran/TreeSim",
  "RemoteRef": "HEAD",
  "RemoteSha": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
  "MD5sum": "2ef61e46c45a1063c9700fc4da60098d",
  "_user": "tanja819",
  "_type": "src",
  "_file": "TreeSim_2.4.tar.gz",
  "_fileid": "c2663b4db49af48d1758482db02b017a4d26848fa16fd361e4b51132ea4ea1ae",
  "_filesize": 169567,
  "_sha256": "c2663b4db49af48d1758482db02b017a4d26848fa16fd361e4b51132ea4ea1ae",
  "_created": "2026-05-12T06:42:05.000Z",
  "_published": "2026-05-22T10:57:35.133Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77365958495,
      "time": 147,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6937423694"
    },
    {
      "job": 77365957848,
      "time": 140,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6937422123"
    },
    {
      "job": 77365958307,
      "time": 171,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6937423358"
    },
    {
      "job": 77365957798,
      "time": 253,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6937437503"
    },
    {
      "job": 77365957681,
      "time": 159,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6937386087"
    },
    {
      "job": 77365957456,
      "time": 105,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158844645"
    },
    {
      "job": 77365958074,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6937410947"
    },
    {
      "job": 77365958282,
      "time": 112,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6937415875"
    },
    {
      "job": 77365957903,
      "time": 102,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6937412531"
    }
  ],
  "_buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/TreeSim",
  "_commit": {
    "id": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
    "author": "Tanja Stadler <tanja.stadler@bsse.ethz.ch>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.4\n",
    "time": 1554738776
  },
  "_maintainer": {
    "name": "Tanja Stadler",
    "email": "tanja.stadler@bsse.ethz.ch",
    "login": "tanja819",
    "uuid": 8371380
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "ape",
      "role": "Depends"
    },
    {
      "package": "geiger",
      "role": "Depends"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 3,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "tanja819",
      "count": 5,
      "uuid": 8371380
    }
  ],
  "_userbio": {
    "uuid": 8371380,
    "type": "user",
    "name": "tanja819"
  },
  "_downloads": {
    "count": 2975,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TreeSim"
  },
  "_mentions": 24,
  "_searchresults": 406,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/TreeSim.html",
    "manual.pdf"
  ],
  "_realowner": "tanja819",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2010-02-23"
    },
    {
      "version": "1.1",
      "date": "2011-03-20"
    },
    {
      "version": "1.3",
      "date": "2011-05-10"
    },
    {
      "version": "1.4",
      "date": "2011-06-15"
    },
    {
      "version": "1.5",
      "date": "2011-11-02"
    },
    {
      "version": "1.6",
      "date": "2012-08-05"
    },
    {
      "version": "1.7",
      "date": "2012-11-20"
    },
    {
      "version": "1.8",
      "date": "2013-04-16"
    },
    {
      "version": "1.9",
      "date": "2013-06-09"
    },
    {
      "version": "1.9.1",
      "date": "2013-12-10"
    },
    {
      "version": "2.0",
      "date": "2014-07-28"
    },
    {
      "version": "2.1",
      "date": "2014-09-18"
    },
    {
      "version": "2.2",
      "date": "2015-10-05"
    },
    {
      "version": "2.3",
      "date": "2017-03-20"
    },
    {
      "version": "2.4",
      "date": "2019-04-08"
    }
  ],
  "_exports": [
    "corsim",
    "cuttree",
    "getx",
    "LTT.plot",
    "LTT.plot.gen",
    "sim.bd.age",
    "sim.bd.taxa",
    "sim.bd.taxa.age",
    "sim.bdsky.stt",
    "sim.bdtypes.stt.taxa",
    "sim.genespeciestree",
    "sim.genetree",
    "sim.gsa.taxa",
    "sim.rateshift.taxa"
  ],
  "_help": [
    {
      "page": "TreeSim-package",
      "title": "TreeSim: Simulating Phylogenetic Trees",
      "topics": [
        "TreeSim-package",
        "TreeSim"
      ]
    },
    {
      "page": "corsim",
      "title": "corsim: Simulating the missing speciation events in an incomplete phylogenies.",
      "topics": [
        "corsim"
      ]
    },
    {
      "page": "cuttree",
      "title": "cuttree: Cutting off the tree to prune recent branches.",
      "topics": [
        "cuttree"
      ]
    },
    {
      "page": "getx",
      "title": "getx: Calculating the vector of speciation / transmission times and sampling times for a phylogenetic tree.",
      "topics": [
        "getx"
      ]
    },
    {
      "page": "LTT.plot",
      "title": "LTT.plot: Plots the lineages through time of a set of phylogenetic trees.",
      "topics": [
        "LTT.plot"
      ]
    },
    {
      "page": "LTT.plot.gen",
      "title": "LTT.plot.gen: Calculates the number of lineages through time for each input tree, as well as the average number of lineages over all trees.",
      "topics": [
        "LTT.plot.gen"
      ]
    },
    {
      "page": "sim.bd.age",
      "title": "sim.bd.age: Simulating birth-death trees of a fixed age.",
      "topics": [
        "sim.bd.age"
      ]
    },
    {
      "page": "sim.bd.taxa",
      "title": "sim.bd.taxa: Simulating birth-death trees on a fixed number of extant taxa.",
      "topics": [
        "sim.bd.taxa"
      ]
    },
    {
      "page": "sim.bd.taxa.age",
      "title": "sim.bd.taxa.age: Simulating birth-death trees with a given age on a fixed number of extant taxa.",
      "topics": [
        "sim.bd.taxa.age"
      ]
    },
    {
      "page": "sim.bdsky.stt",
      "title": "sim.bdsky.stt: Simulating sequentially sampled birth-death, SIS, SIR or SIRS trees where birth and death rates are changing through time.",
      "topics": [
        "sim.bdsky.stt"
      ]
    },
    {
      "page": "sim.bdtypes.stt.taxa",
      "title": "sim.bdtypes.stt.taxa: Simulating multitype birth-death trees with a fixed number of tips sampled through time.",
      "topics": [
        "sim.bdtypes.stt.taxa"
      ]
    },
    {
      "page": "sim.genespeciestree",
      "title": "sim.genespeciestree: Simulating birth-death species trees with nested coalescent gene trees.",
      "topics": [
        "sim.genespeciestree"
      ]
    },
    {
      "page": "sim.genetree",
      "title": "sim.genetree: Simulating coalescent gene trees.",
      "topics": [
        "sim.genetree"
      ]
    },
    {
      "page": "sim.gsa.taxa",
      "title": "sim.gsa.taxa: Sampling trees on n tips from bigger trees.",
      "topics": [
        "sim.gsa.taxa"
      ]
    },
    {
      "page": "sim.rateshift.taxa",
      "title": "sim.rateshift.taxa: Simulating trees incorporating mass extinction events and rate shifts.",
      "topics": [
        "sim.rateshift.taxa"
      ]
    }
  ],
  "_rundeps": [
    "ape",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "colorspace",
    "combinat",
    "cpp11",
    "DEoptim",
    "deSolve",
    "digest",
    "doParallel",
    "expm",
    "fastmatch",
    "foreach",
    "geiger",
    "generics",
    "glue",
    "igraph",
    "iterators",
    "lattice",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "mnormt",
    "mvtnorm",
    "ncbit",
    "nlme",
    "numDeriv",
    "optimParallel",
    "phangorn",
    "phytools",
    "pkgconfig",
    "quadprog",
    "Rcpp",
    "rlang",
    "scatterplot3d",
    "subplex",
    "vctrs"
  ],
  "_score": 5.0362555130810875,
  "_indexed": true,
  "_nocasepkg": "treesim",
  "_universes": [
    "tanja819"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.4",
      "date": "2026-05-12T06:44:12.000Z",
      "distro": "noble",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "d8e0c944c57056907ab597b7b1a98e46821e9533b4e3652615465d0c9b58c8e1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.4",
      "date": "2026-05-12T06:44:09.000Z",
      "distro": "noble",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "7d74b7691c361d47724d37eeeee9bf26ae82414a9781d4f4117643da3dc6f1be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.4",
      "date": "2026-05-12T06:44:25.000Z",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "f1fe49f5021d492fede0ebf687dbe2eadb5f55f8f7836522f88c49e07806bbf0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.4",
      "date": "2026-05-12T06:45:03.000Z",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "38a304992f7c0a50a6f93a13d8c325621b026287ed4286e0378a8fca4d8a03b9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.4",
      "date": "2026-05-12T06:43:19.000Z",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "77313f32f79c19b18897ed19ba1fc2519bdfab15484929a794391363e0f1f136",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.4",
      "date": "2026-05-12T06:43:39.000Z",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "af43cd23e3fa29c480f0fe57bb258b3e50508405f3d9de076315f523bb3afdcb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.4",
      "date": "2026-05-12T06:43:23.000Z",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "07cff535b2c5f60af45b51d0672ddc6ff4ef335ee16ee7a1f7429c019c02a9c0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.4",
      "date": "2026-05-22T10:57:14.000Z",
      "commit": "b78f72af95b2ef85bddcaf4e333afb02038074a4",
      "fileid": "777ed76cd87380085fb78fb22182b0d034c466cab23e5089dd0926fbb3e6dc9e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/tanja819/actions/runs/25717980500"
    }
  ]
}