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type: software
license: GPL-2.0-only
title: 'TreePar: Estimating Birth and Death Rates Based on Phylogenies'
version: '3.3'
doi: 10.32614/CRAN.package.TreePar
abstract: (i) For a given species phylogeny on present day data which is calibrated
  to calendar-time, a method for estimating maximum likelihood speciation and extinction
  processes is provided. The method allows for non-constant rates. Rates may change
  (1) as a function of time, i.e. rate shifts at specified times or mass extinction
  events (likelihood implemented as LikShifts(), optimization as bd.shifts.optim()
  and visualized as bd.shifts.plot()) or (2) as a function of the number of species,
  i.e. density-dependence (likelihood implemented as LikDD() and optimization as bd.densdep.optim())
  or (3) extinction rate may be a function of species age (likelihood implemented
  as LikAge() and optimization as bd.age.optim.matlab()). Note that the methods take
  into account the whole phylogeny, in particular it accounts for the "pull of the
  present" effect. (1-3) can take into account incomplete species sampling, as long
  as each species has the same probability of being sampled. For a given phylogeny
  on higher taxa (i.e. all but one species per taxa are missing), where the number
  of species is known within each higher taxa, speciation and extinction rates can
  be estimated under model (1) (implemented within LikShifts() and bd.shifts.optim()
  with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g.
  a virus phylogeny, rates can be estimated under a model where rates vary across
  time using bdsky.stt.optim() based on likelihood LikShiftsSTT() (extending LikShifts()
  and bd.shifts.optim()). Furthermore, rates may vary as a function of host types
  using LikTypesSTT() (multitype branching process extending functions in R package
  diversitree). This function can furthermore calculate the likelihood under an epidemiological
  model where infected individuals are first exposed and then infectious.
authors:
- family-names: Stadler
  given-names: Tanja
  email: tanja.stadler@bsse.ethz.ch
repository: https://phylotastic.r-universe.dev
commit: 77d33da3f37f757e8547cae5c4b072341cf8db10
date-released: '2015-01-02'
contact:
- family-names: Stadler
  given-names: Tanja
  email: tanja.stadler@bsse.ethz.ch