| ltt {phytools} | R Documentation |
This function computes LTT plot with extant and extinct lineages, and optionally conducts γ-test of Pybus & Harvey (2000). The object returned by ltt can be plotted or re-plotted using plot.
ltt(tree, plot=TRUE, drop.extinct=FALSE, log.lineages=TRUE, gamma=TRUE, ...)
tree |
is a phylogenetic tree in |
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 |
Although it is calculated here, it's unclear how to interpret the γ-statistic if not all the tips in the tree are contemporaneous.
An object of class "ltt" which includes 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. |
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".
Liam Revell liam.revell@umb.edu
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