Creates lineage-through-time plot (including extinct lineages).
ltt(): This function takes a "phylo" tree object and returns a list of branching times and number of lineages at each branch time.
Input
result<-ltt(ree,plot=TRUE,drop.extinct=FALSE,log.lineages=TRUE,gamma=TRUE)
"tree" is a phylogenetic tree in modified "phylo" format.
function optionally creates a ltt plot; also can drop extinct taxa from the tree; plot log(lineages); and compute the gamma statistic & p-value.
Output
ltt() outputs a list with the following elements:
"$times" a vector of branching times;
"$ltt" a vector of lineages; and (optionally)
"$gamma" value of the gamma-statistic;
"$p" two-tailed p-value for gamma.
Citation
Function written by Liam J. Revell 2010/2011.
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., L. J. Harmon, and R. E. Glor. 2005. Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. Systematic Biology 54: 973-983.
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Last modified May 1, 2011.