-## ltt.plot.R (2008-02-22)
+## ltt.plot.R (2009-05-10)
## Lineages Through Time Plot
-## Copyright 2002-2008 Emmanuel Paradis
+## Copyright 2002-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
ltt.plot <- function(phy, xlab = "Time", ylab = "N", ...)
{
- if (class(phy) != "phylo") stop('object "phy" is not of class "phylo"')
+ if (!inherits(phy, "phylo")) stop('object "phy" is not of class "phylo"')
+ if (!is.binary.tree(phy)) phy <- multi2di(phy)
time <- sort(branching.times(phy), decreasing = TRUE)
N <- 1:(length(time) + 1)
plot.default(-c(time, 0), N, xlab = xlab, ylab = ylab,
ltt.lines <- function(phy, ...)
{
+ if (!is.binary.tree(phy)) phy <- multi2di(phy)
time <- sort(branching.times(phy), decreasing = TRUE)
N <- 1:(length(time) + 1)
lines(-c(time, 0), N, type = "S", ...)
xlab = "Time", ylab = "N", log = "")
{
ltt.xy <- function(phy) {
+ if (!is.binary.tree(phy)) phy <- multi2di(phy)
x <- -c(sort(branching.times(phy), decreasing = TRUE), 0)
names(x) <- NULL
y <- 1:length(x)
cbind(x, y)
}
- if (class(phy) == "phylo") {
+ if (inherits(phy, "phylo")) { # if a tree of class "phylo"
TREES <- list(ltt.xy(phy))
names(TREES) <- deparse(substitute(phy))
} else { # a list of trees