method allows for non-constant rates. Rates may change (i) as a
function of time (rate shifts at specified times or mass
extinction events) or (ii) as a function of the number of
species (density-dependence). Note that the method takes into

Title: Estimating speciation and extinction rates based on phylogenies

Package: TreePar
Type: Package
Title: Estimating speciation and extinction rates based on phylogenies
Version: 2.1.2
Date: 2011-08-22
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@env.ethz.ch>
Depends: ape, Matrix, subplex, TreeSim
Description: 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 (i) as a
function of time, i.e. rate shifts at specified times or mass
extinction events (implemented as bd.shifts.optim) or (ii) 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. For a given phylogeny on
higher taxa, but where the number of species is known within
each higher taxa, speciation and extinction rates can be
estimated, under the assumption that these rates remained
constant (implemented as bd.groups.optim).
License: GPL-2
LazyLoad: yes
Packaged: 2011-08-23 11:17:18 UTC; tanja
Repository: CRAN
Date/Publication: 2011-08-23 20:02:49

Package: TreePar
Type: Package
Title: Estimating speciation and extinction rates based on phylogenies
Version: 2.1
Date: 2011-07-12
Author: Tanja Stadler
Maintainer: Tanja Stadler <tanja.stadler@env.ethz.ch>
Depends: ape, Matrix, subplex, TreeSim
Description: 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 (i) as a
function of time, i.e. rate shifts at specified times or mass
extinction events (implemented as bd.shifts.optim) or (ii) 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. For a given phylogeny on
higher taxa, but where the number of species is known within
each higher taxa, speciation and extinction rates can be
estimated, under the assumption that these rates remained
constant (implemented as bd.groups.optim).
License: GPL-2
LazyLoad: yes
Packaged: 2011-07-13 10:38:33 UTC; tanja
Repository: CRAN
Date/Publication: 2011-07-23 13:04:47