ape (version 1.1-2)

ltt.plot: 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".

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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