phytools (version 2.1-1)

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

Description

Computes and visualizes a lineage through time (LTT) plot, and related measures.

Usage

ltt(tree, ...)
# S3 method for phylo
ltt(tree, plot=TRUE, drop.extinct=FALSE, log.lineages=TRUE, gamma=TRUE, ...)
# S3 method for multiPhylo
ltt(tree, drop.extinct=FALSE, gamma=TRUE, ...)
# S3 method for simmap
ltt(tree, plot=TRUE, log.lineages=FALSE, gamma=TRUE, ...)
# S3 method for multiSimmap
ltt(tree, gamma=TRUE, ...)
gtt(tree, n=100, ...)
mccr(obj, rho=1, nsim=100, ...)

Value

ltt returns an object of class "ltt" which normally includes the following elements:

times

a vector of branching times.

ltt

a vector of lineages, or a matrix of lineages in each state over time for objects of class "simmap" and "multiSimmap".

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".

gtt returns an object of class "gtt".

mccr returns of object of class "mccr".

Arguments

tree

an object of class "phylo", "multiPhylo", "simmap", or "multiSimmap".

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 for "phylo" and "multiPhylo" objects) or linear-linear scale.

gamma

logical value indicating whether or not to compute \(\gamma\) from Pybus & Harvey (2000; Proc. Roy. Soc. B).

n

for gtt the number of time intervals to use to track \(\gamma\) 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.

Author

Liam Revell

Details

The function ltt 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.

For the case in which tree is an object of class "simmap" or "multiSimmap" then the object will contain the number of lineages through time (for each tree, in the case of "multiSimmap" objects) separated by mapped regimes.

The function gtt computes the value of Pybus & Harvey's \(\gamma\) 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 \(\gamma\) statistic.

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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

gammatest, ltt95

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)