get.groups: get.groups: Generates input for bd.shifts.optim when...

In TreePar: Estimating birth and death rates based on phylogenies

Description

get.groups generates input for bd.shifts.optim if the phylogeny is not resolved on the species level (groups!=0).

Usage

get.groups(tree,S,xcut=0)

Arguments

tree	Phylogenetic tree to be analyzed with bd.shifts.optim.
S	S[i]: Number of species in tree represented by leaf i.
xcut	Age of the higher taxa. If xcut=0: age of higher taxa is the length of the edge corresponding to the higher taxa. If xcut>0: age of each higher taxa is xcut.

Author(s)

Tanja Stadler

References

T. Stadler, F. Bokma. Estimating speciation and extinction rates for phylogenies of higher taxa. Syst. Biol., 62(2): 220-230, 2013.

Examples

# see manual of bd.shifts.optim()

TreePar documentation built on May 1, 2019, 9:20 p.m.