This function computes LTT plot with extant and extinct lineages, and optionally conducts $\gamma$-test of Pybus & Harvey (2000). The object returned by ltt can be plotted or re-plotted using plot.
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 eqngamma from Pybus & Harvey (2000; Proc. Roy. Soc. B).
...
other arguments to be passed to plotting methods. See plot.default.
Value
An object of class "ltt" which includes the following components:If tree is an object of class "multiPhylo", then an object of class "multiLtt" is returned consisting of a list of object of class "ltt".
Details
Although it is calculated here, it's unclear how to interpret the $\gamma$-statistic if not all the tips in the tree are contemporaneous.
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.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
trees<-pbtree(n=100,scale=100,nsim=10)
obj<-ltt(trees,plot=FALSE)
plot(obj,log="y",log.lineages=FALSE,main="lineage through time plots")
tree<-pbtree(b=1,d=0.25,t=4)
obj<-ltt(tree,gamma=FALSE)
obj