ltt.plot {ape}R Documentation

Lineages Through Time Plot

Description

This function plots, on the current graphical device, the minimum numbers of lineages through time from a phylogenetic tree.

Usage

ltt.plot(phy, ...)

Arguments

phy an object of class "phylo".
... further arguments to be passed to plot() (see Details: on how to transform the axes).

Details

The y-axis can be log-transformed by adding the following option: log = "y".

Author(s)

Emmanuel Paradis paradis@isem.univ-montp2.fr

References

Harvey, P. H., May, R. M. and Nee, S. (1994) Phylogenies without fossils. Evolution, 48, 523–529.

Nee, S., Holmes, E. C., Rambaut, A. and Harvey, P. H. (1995) Inferring population history from molecular phylogenies. Philosophical Transactions of the Royal Society of London. Series B. Biological Sciences, 349, 25–31.

See Also

skyline, branching.times, birthdeath, plot for the basic plotting function in R

Examples

data(bird.families)
data(bird.orders)
opar <- par(mfrow = c(2, 1))
ltt.plot(bird.families)
title("Lineages Through Time Plot of the Bird Families")
ltt.plot(bird.families, log = "y")
title(main = "Lineages Through Time Plot of the Bird Families",
      sub = "(with logarithmic transformation of the y-axis)")
par(opar)

### to plot the tree and the LTT plot together
tmp <- bird.families
tmp$tip.label <- rep("", length(bird.families$tip.label))
tmp2 <- bird.orders
tmp2$tip.label <- rep("", length(bird.orders$tip.label))
layout(matrix(1:4, 2, 2))
plot(tmp)
ltt.plot(bird.families, main = "Bird families")
plot(tmp2)
ltt.plot(bird.orders, main = "Bird orders")

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