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:
- timesa vector of branching times.
- ltta vector of linages.
- gammaoptionally, a value for the gamma-statistic.
- ptwo-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.