treemrca

Vector of speciation times in the phylogeny. Time is measured increasing going into the past with the present being time 0. x can be obtained from a phylogenetic tree using getx(TREE).

The time of rate shifts (t[1]=0 is required, being the present)

Vectors of the same length as t. l[i] (resp. mu[i]) specifies the speciation (resp. extinction rate) prior to t[i].

l,mu

Vector of length m. sampling_i is the probability of a species surviving the mass extinction at time t_i. sampling_1 is the probability of an extant species being sampled. sampling_1=1 means that the considered phylogeny is complete. sampling_i=1 (i>1) me

sampling

Not relevant when using treemrca without optimizing (for bd.shifts.optim: posdiv=FALSE (default) allows the speciation - extinction rate to be negative, i.e. allows for periods of declining diversity. posdiv=TRUE forces the speciation - extinction rate to

posdiv

treemrca: calculates the likelihood of a tree given the speciation and extinction rates and shift times.

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).

treemrca: treemrca: calculates the likelihood of a tree

Description

Usage

Arguments

Value

References