## TreePar: Estimating birth and death rates based on phylogenies

(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).

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