{
  "_id": "6a103f18acfb0bcc41c9cbc8",
  "Package": "TreePar",
  "Type": "Package",
  "Title": "Estimating Birth and Death Rates Based on Phylogenies",
  "Version": "3.3",
  "Date": "2015-01-02",
  "Author": "Tanja Stadler",
  "Maintainer": "Tanja Stadler <tanja.stadler@bsse.ethz.ch>",
  "Description": "(i) For a given species phylogeny on present day data\nwhich is calibrated to calendar-time, a method for estimating\nmaximum likelihood speciation and extinction processes is\nprovided. The method allows for non-constant rates. Rates may\nchange (1) as a function of time, i.e. rate shifts at specified\ntimes or mass extinction events (likelihood implemented as\nLikShifts(), optimization as bd.shifts.optim() and visualized\nas bd.shifts.plot()) or (2) as a function of the number of\nspecies, i.e. density-dependence (likelihood implemented as\nLikDD() and optimization as bd.densdep.optim()) or (3)\nextinction rate may be a function of species age (likelihood\nimplemented as LikAge() and optimization as\nbd.age.optim.matlab()). Note that the methods take into account\nthe whole phylogeny, in particular it accounts for the \"pull of\nthe present\" effect. (1-3) can take into account incomplete\nspecies sampling, as long as each species has the same\nprobability of being sampled. For a given phylogeny on higher\ntaxa (i.e. all but one species per taxa are missing), where the\nnumber of species is known within each higher taxa, speciation\nand extinction rates can be estimated under model (1)\n(implemented within LikShifts() and bd.shifts.optim() with\ngroups !=0). (ii) For a given phylogeny with sequentially\nsampled tips, e.g. a virus phylogeny, rates can be estimated\nunder a model where rates vary across time using\nbdsky.stt.optim() based on likelihood LikShiftsSTT() (extending\nLikShifts() and bd.shifts.optim()). Furthermore, rates may vary\nas a function of host types using LikTypesSTT() (multitype\nbranching process extending functions in R package\ndiversitree). This function can furthermore calculate the\nlikelihood under an epidemiological model where infected\nindividuals are first exposed and then infectious.",
  "License": "GPL-2",
  "LazyLoad": "yes",
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  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2016-07-13 19:44:56 UTC",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "_published": "2026-05-22T11:33:44.671Z",
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    "author": "Stadler  Tanja <tstadler@bs-mba05.d.ethz.ch>",
    "committer": "Stadler  Tanja <tstadler@bs-mba05.d.ethz.ch>",
    "message": "TreePar finally on git\n",
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    "email": "tanja.stadler@bsse.ethz.ch",
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    "bd.shifts.plot",
    "bdsky.stt.optim",
    "create.mat",
    "get.groups",
    "LikAge",
    "LikConstant",
    "LikConstantn",
    "LikDD",
    "LikShifts",
    "LikShiftsPP",
    "LikShiftsSTT",
    "LikTypesSTT"
  ],
  "_help": [
    {
      "page": "TreePar-package",
      "title": "Estimating Birth and Death Rates Based on Phylogenies",
      "topics": [
        "TreePar-package",
        "TreePar"
      ]
    },
    {
      "page": "addroot",
      "title": "addroot: Adds a root edge ancestral to the first branching event.",
      "topics": [
        "addroot"
      ]
    },
    {
      "page": "bd.age.optim.matlab",
      "title": "bd.age.optim.matlab: Estimating speciation rate and age-dependent extinction rate in phylogenies.",
      "topics": [
        "bd.age.optim.matlab"
      ]
    },
    {
      "page": "bd.densdep.optim",
      "title": "bd.densdep.optim: Estimating maximum likelihood speciation and extinction rates in phylogenies under a density-dependent speciation model.",
      "topics": [
        "bd.densdep.optim"
      ]
    },
    {
      "page": "bd.shifts.optim",
      "title": "bd.shifts.optim: Estimating speciation and extinction rate changes and mass extinction events in phylogenies.",
      "topics": [
        "bd.shifts.optim"
      ]
    },
    {
      "page": "bd.shifts.plot",
      "title": "bd.shifts.plot: Plots the diversification rate estimates obtained with the function bd.shifts.optim.",
      "topics": [
        "bd.shifts.plot"
      ]
    },
    {
      "page": "bdsky.stt.optim",
      "title": "bdsky.stt.optim: Estimating piecewise constant birth and death rates in phylogenies with sequentially sampled tips.",
      "topics": [
        "bdsky.stt.optim"
      ]
    },
    {
      "page": "create.mat",
      "title": "create.mat: Generates input for LikAge and bd.age.optim.matlab.",
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        "create.mat"
      ]
    },
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      "page": "get.groups",
      "title": "get.groups: Generates input for bd.shifts.optim when groups!=0.",
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      ]
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      "page": "LikAge",
      "title": "LikAge: Calculates the likelihood of speciation and extinction rates for an ultrametric phylogeny under an age-dependent extinction model conditioning on the age of the tree.",
      "topics": [
        "LikAge"
      ]
    },
    {
      "page": "LikConstant",
      "title": "LikConstant: Calculates the likelihood of constant birth and death rates for a given phylogenetic tree.",
      "topics": [
        "LikConstant"
      ]
    },
    {
      "page": "LikConstantn",
      "title": "LikConstantn: Calculates the likelihood of constant birth and death rates for a given phylogenetic tree.",
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      ]
    },
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      "page": "LikDD",
      "title": "LikDD: Calculates the likelihood of speciation and extinction rates for an ultrametric phylogeny under a density-dependent speciation model conditioning on the age of the tree.",
      "topics": [
        "LikDD"
      ]
    },
    {
      "page": "LikShifts",
      "title": "LikShifts: Calculates the likelihood of time-dependent birth and death rates given a phylogenetic tree.",
      "topics": [
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      ]
    },
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      "page": "LikShiftsPP",
      "title": "LikShiftsPP: Calculates the likelihood of time-dependent birth and death rates given a phylogenetic tree.",
      "topics": [
        "LikShiftsPP"
      ]
    },
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      "page": "LikShiftsSTT",
      "title": "LikShiftsSTT: Calculates likelihood of piecewise constant birth and death rates for a given phylogenetic tree with sequentially sampled tips.",
      "topics": [
        "LikShiftsSTT"
      ]
    },
    {
      "page": "LikTypesSTT",
      "title": "LikTypesSTT: Calculates the likelihood of the 2-type birth-death model parameters for a given tree.",
      "topics": [
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      ]
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