get.groups: Generates input for bd.shifts.optim when groups!=0.

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Description

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

Usage

1
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

1
# see manual of bd.shifts.optim()