ltt.plot: Lineages Through Time Plot

Description

These functions plot, on the current graphical device, the minimum numbers of lineages through time from phylogenetic trees.

Usage

ltt.plot(phy, xlab = "Time", ylab = "N", ...)
ltt.lines(phy, ...)
mltt.plot(phy, ..., dcol = TRUE, dlty = FALSE,
          legend = TRUE, xlab = "Time", ylab = "N")

Arguments

phy

an object of class "phylo"; this could be an object of class c("multi.tree", "phylo") in the case of mltt.plot.

xlab

a character string (or a variable of mode character) giving the label for the x-axis (default is "Time").

ylab

idem for the y-axis (default is "N").

...

in the cases of ltt.plot() and ltt.lines() these are further (graphical) arguments to be passed to plot() or lines(), respectively (see Details: on how to transform the axes); in

dcol

a logical specifying whether the different curves should be differentiated with colors (default is TRUE).

dlty

a logical specifying whether the different curves should be differentiated with patterns of dots and dashes (default is FALSE).

legend

a logical specifying whether a legend should be plotted.

Details

ltt.plot does a simple lineages through time (LTT) plot. Additional arguments (...) may be used to change, for instance, the limits on the axes (with xlim and/or ylim) or other graphical settings (col for the color, lwd for the line thickness, lty for the line type may be useful; see par for an exhaustive listing of graphical parameters). The $y$-axis can be log-transformed by adding the following option: log = "y".

ltt.lines adds a LTT curve to an existing plot. Additional arguments (...) may be used to change the settings of the added line. Of course, the settings of the already existing LTT plot cannot be altered this way.

mltt.plot does a multiple LTT plot taking as arguments one or several trees. These trees may be given as objects of class "phylo" (single trees) or c("multi.tree", "phylo") (multiple trees). Any number of objects may be given. This function is mainly for exploratory analyses with the advantages that the axes are set properly to view all lines, and the legend is plotted by default. For more flexible settings of line drawings, it is probably better to combine ltt.plot() with successive calls of ltt.lines() (see Examples:).

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.

Examples

Run this code

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
layout(matrix(1:4, 2, 2))
plot(bird.families, show.tip.label = FALSE)
ltt.plot(bird.families, main = "Bird families")
plot(bird.orders, show.tip.label = FALSE)
ltt.plot(bird.orders, main = "Bird orders")
layout(matrix(1))
mltt.plot(bird.families, bird.orders)
### Generates 10 random trees with 23 tips:
TR <- replicate(10, rcoal(23), FALSE)
### Give names to each tree:
names(TR) <- paste("random tree", 1:10)
### And specify the class of the list so that mltt.plot()
### does not trash it!
class(TR) <- c("multi.tree", "phylo")
mltt.plot(TR)
### And now for something (not so) completely different:
ltt.plot(bird.orders, lwd = 2)
lapply(TR, ltt.lines, lty = 2) # same as:
### for (i in 1:10) ltt.lines(TR[[i]], lty = 2)
legend(-10, 5, lwd = c(2, 1), lty = c(1, 2), bty = "n",
       legend = c("Bird orders", "Random trees"))

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