fixing drop.tip and bionj

[ape.git] / R / ltt.plot.R

diff --git a/R/ltt.plot.R b/R/ltt.plot.R
index 2a0179c4d6538fa294674dde6cfaffb603711fe4..a7eae04323169877a30c86b15984fa2256936e77 100644 (file)
--- a/R/ltt.plot.R
+++ b/R/ltt.plot.R
@@ -1,15 +1,16 @@
-## 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,
@@ -18,6 +19,7 @@ ltt.plot <- function(phy, xlab = "Time", ylab = "N", ...)
 
 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", ...)
@@ -27,12 +29,13 @@ mltt.plot <- function(phy, ..., dcol = TRUE, dlty = FALSE, legend = TRUE,
                       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