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>
Depends: ape, Matrix, subplex, TreeSim (>= 2.1), deSolve
Description: (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.
License: GPL-2
LazyLoad: yes
Config/pak/sysreqs: libglpk-dev make libxml2-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2016-07-13 19:44:56 UTC
RemoteUrl: https://github.com/tanja819/TreePar
RemoteRef: HEAD
RemoteSha: 77d33da3f37f757e8547cae5c4b072341cf8db10
NeedsCompilation: no
Packaged: 2026-10-08 08:40:08 UTC; root
Built: R 4.5.3; ; 2026-10-08 08:41:19 UTC; windows
