getx

datatree

getx calculates the input vector x for the rate estimation functions from a phylogenetic tree (which may have polytomies)

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).

getx: getx: Getting the vector of speciation times x from a phylogenetic tree

Description

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References