scaleBranchingtimes {laser} | R Documentation |
Scales a vector of branching times by a known basal divergence time.
scaleBranchingtimes(x, basal = 100)
x |
a numeric vector of branching times |
basal |
estimated time of the basal divergence for the clade |
This function can be used when analyzing branching times for which it is possible to estimate the basal divergence time. If branch lengths in a specified phylogenetic tree are given in units of genetic distance, but the basal divergence is estimated at Z mya, call res <- scaleBranchingtimes(x, basal = Z). Rate parameters estimated by fitting variants of birth-death models will then be in units of lineage births or deaths per million years.
a vector of scaled branching times
Dan Rabosky DLR32@cornell.edu
data(plethodon) # suppose plethodon basal divergence occurred 23 mya: svec <- scaleBranchingtimes(plethodon, basal = 23) plotLtt(svec) # plots lineages through time in units of time, rather than genetic # distance pureBirth(svec) # returns speciation rate in units of lineages/million years