phytools (version 0.1-0)

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.

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:
• times
  a vector of branching times.
• ltt
  a vector of linages.
• gamma
  optionally, a value for the gamma-statistic.
• p
  two-tailed P-value for the gamma-test.

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.

See Also

gammatest

Examples

tree<-rbdtree(birth=1,death=0,Tmax=4)
  ltt(tree)
  tree<-rlineage(birth=1,death=0.25,Tmax=4)
  ltt(tree,gamma=FALSE)