ltt: Creates lineage-through-time plot (including extinct lineages)

Description

This function computes LTT plot with extant and extinct lineages, and optionally conducts gamma-test of Pybus & Harvey (2000).

Usage

ltt(tree,plot=TRUE,drop.extinct=FALSE,log.lineages=TRUE,gamma=TRUE)

Arguments

tree

is a phylogenetic tree in "phylo" format, or an object of class "multiPhylo" containing a list of phylogenetic trees.

plot

a logical value indicating whether or not to create LTT plot.

drop.extinct

logical value indicating whether or not to drop extinct tips from the tree.

log.lineages

logical value indicating whether LTT plot should be on log-linear (default) or linear-linear scale.

gamma

logical value indicating whether or not to compute gamma from Pybus & Harvey (2000; Proc. Roy. Soc. B).

Value

a list with the following components:
timesa vector of branching times.
ltta vector of linages.
gammaoptionally, a value for the gamma-statistic.
ptwo-tailed P-value for the gamma-test.
If tree is an object of class "multiPhylo", a list of the above list will be returned.

References

Pybus, O. G., and P. H. Harvey. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B, 267, 2267-2272.

Examples

Run this code

trees<-pbtree(n=100,scale=100,nsim=10)
  ltt(trees,log.lineages=FALSE)
  tree<-rlineage(birth=1,death=0.25,Tmax=4)
  ltt(tree,gamma=FALSE)