Package: TreePar
Type: Package
Title: Estimating birth and death rates based on phylogenies
Version: 2.5
Date: 2013-05-07
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@env.ethz.ch>
Depends: ape, Matrix, subplex, TreeSim (>= 1.6), 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 (implemented as bd.shifts.optim
and visualized as bd.shifts.plot) or (2) as a function of the
number of species, i.e. density-dependence (implemented as
bd.densdep.optim). Note that the method takes into account the
whole phylogeny, in particular it accounts for the "pull of the
present" effect. Both models 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 mission), but where
the number of species is known within each higher taxa,
speciation and extinction rates can be estimated under model
(1) (implemented as 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 (extending
bd.shifts.optim). Furthermore rates may vary as a function of
host types using bdtypes.stt.lik (multitype branching process
extending functions in R package diversitree).
License: GPL-2
LazyLoad: yes
Packaged: 2013-06-09 16:28:20 UTC; tanja
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-06-09 19:39:34

Depends: ape, Matrix, subplex, TreeSim (>= 2.0), 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). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. Both (1) and (2) 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).