phytools: ltt – R documentation

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ltt

Creates lineage-through-time plot (including extinct lineages)

Description

The function ltt 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.

The function gtt computes the value of Pybus & Harvey's γ statistic through time by slicing the tree at various points - by default in even intervals from the time above the root at which N = 3 to the present day.

The function mccr performs the MCCR test of Pybus & Harvey (2000) which takes into account incomplete taxon sampling in computing a P-value of the γ statistic.

Usage

ltt(tree, plot=TRUE, drop.extinct=FALSE, log.lineages=TRUE, gamma=TRUE, ...)
gtt(tree, n=100, ...)
mccr(obj, rho=1, nsim=100, ...)

Arguments

`tree`	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 γ from Pybus & Harvey (2000; Proc. Roy. Soc. B).
`n`	for `gtt` the number of time intervals to use to track γ through time.
`obj`	for `mccr` an object of class `"ltt"`.
`rho`	for `mccr` sampling fraction.
`nsim`	for `mccr` number of simulations to use for the MCCR test.
`...`	other arguments to be passed to plotting methods. See `plot.default`.

Details

Although it is calculated here, it's unclear how to interpret the γ-statistic if not all the tips in the tree are contemporaneous.

Value

ltt returns 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 γ-statistic.
`p`	two-tailed P-value for the γ-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".

gtt returns an object of class "gtt".

mccr returns of object of class "mccr".

Author(s)

Liam Revell liam.revell@umb.edu

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.

Examples

## LTT plots
set.seed(99)
trees<-pbtree(n=100,scale=100,nsim=10)
obj<-ltt(trees,plot=FALSE)
plot(obj,log="y",log.lineages=FALSE,
    bty="l")
title(main="LTT plots for 10 pure-birth trees",
    font.main=3)
tree<-pbtree(b=1,d=0.25,t=4)
obj<-ltt(tree,gamma=FALSE,show.tree=TRUE,
    bty="l")
title(main="LTT plot with superimposed tree",
    font.main=3)
obj
## GTT plot
data(anoletree)
anole.gtt<-gtt(anoletree,n=40)
plot(anole.gtt)

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19

ltt