ltt.plot: Lineages Through Time Plot

Description

These functions provide tools for plotting the numbers of lineages through time from phylogenetic trees.

Usage

ltt.plot(phy, xlab = "Time", ylab = "N",
         backward = TRUE, tol = 1e-6, ...)
ltt.lines(phy, backward = TRUE, tol = 1e-6, ...)
mltt.plot(phy, ..., dcol = TRUE, dlty = FALSE, legend = TRUE,
          xlab = "Time", ylab = "N", log = "", backward = TRUE,
          tol = 1e-6)
ltt.coplot(phy, backward = TRUE, ...)
ltt.plot.coords(phy, backward = TRUE, tol = 1e-6, type = "S")

Value

ltt.plot.coords returns a two-column matrix with the time points and the number of lineages, respectively.

type = "S" returns the number of lineages to the left of (or "up to") the corresponding point in time, while type = "s" returns the number of lineages to the right of this point (i.e, between that time and the next).

Arguments

phy: an object of class "phylo"; this could be an object of class "multiPhylo" 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").
backward: a logical value: should the time axis be traced from the present (the default), or from the root of the tree?
tol: a numeric value (see details).
...: in the cases of ltt.plot(), ltt.lines(), or ltt.coplot() these are further (graphical) arguments to be passed to plot(), lines(), or plot.phylo(), respectively (see details on how to transform the axes); in the case of mltt.plot() these are additional trees to be plotted (see details).
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.
log: a character string specifying which axis(es) to be log-transformed; must be one of the followings: "", "x", "y", or "xy".
type: either "S" or "s", the preferred type of step function, corresponding to argument type of base function plot(). See section "Value" below.

Author

Emmanuel Paradis

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".

The option tol is used as follows: first the most distant tip from the root is found, then all tips whose distance to the root is not different from the previous one more than tol are considered to be contemporaneous with it.

If the tree is not ultrametric, the plot is done assuming the tips, except the most distant from the root, represent extinction events. If a root edge is present, it is taken into account.

ltt.lines adds a LTT curve to an existing plot. Additional arguments (...) may be used to change the settings of the added line.

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) and/or "multiPhylo" (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. The plot will certainly make sense if all trees have their most-distant-from-the-root tips contemporaneous (i.e., trees with only extinct lineages will not be represented properly). For more flexible settings of line drawings, it may be better to combine ltt.plot() with successive calls of ltt.lines() (see examples).

ltt.coplot is meant to show how to set a tree and a LTT plots on the same scales. All extra arguments modify only the appearance of the tree. The code can be easily edited and tailored.

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)
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
data(bird.orders)
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(1)

### better with ltt.coplot():
ltt.coplot(bird.families, show.tip.label = FALSE, x.lim = 27.5)
data(chiroptera)
chiroptera <- compute.brlen(chiroptera)
ltt.coplot(chiroptera, show.tip.label = FALSE, type = "c")

### with extinct lineages and a root edge:
omar <- par("mar")
set.seed(31)
tr <- rlineage(0.2, 0.15)
tr$root.edge <- 5
ltt.coplot(tr, show.tip.label = FALSE, x.lim = 55)
## compare with:
## ltt.coplot(drop.fossil(tr), show.tip.label = FALSE)
layout(1)
par(mar = omar)

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) <- "multiPhylo"
mltt.plot(TR, bird.orders)
### And now for something (not so) completely different:
ltt.plot(bird.orders, lwd = 2)
for (i in 1:10) ltt.lines(TR[[i]], lty = 2)
legend(-20, 10, lwd = c(2, 1), lty = c(1, 2), bty = "n",
       legend = c("Bird orders", "Random (coalescent) trees"))

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