From 0e8dcca3046844b0b36b4f5855e6c10319db45a2 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Wed, 4 Mar 2009 08:38:20 +0000
Subject: [PATCH] correcting bug in drop.tip

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@64 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 ChangeLog         |  5 +++++
 DESCRIPTION       |  2 +-
 R/drop.tip.R      |  9 +++++----
 man/plot.phylo.Rd | 10 ----------
 4 files changed, 11 insertions(+), 15 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index 2d14a5b..c01a581 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -11,6 +11,11 @@ NEW FEATURES
       Yule model by maximum likelihood.
 
 
+BUG FIXES
+
+    o drop.tip() shuffled tip labels in some cases.
+
+
 
 		CHANGES IN APE VERSION 2.2-4
 
diff --git a/DESCRIPTION b/DESCRIPTION
index e013e3f..65f9a43 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.3
-Date: 2009-02-20
+Date: 2009-03-04
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
   Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
diff --git a/R/drop.tip.R b/R/drop.tip.R
index d819c75..69c9576 100644
--- a/R/drop.tip.R
+++ b/R/drop.tip.R
@@ -1,4 +1,4 @@
-## drop.tip.R (2009-01-07)
+## drop.tip.R (2009-03-04)
 
 ##   Remove Tips in a Phylogenetic Tree
 
@@ -22,7 +22,8 @@ extract.clade <- function(phy, node, root.edge = 0)
             stop("the tree has no node labels")
         node <- which(phy$node.label %in% node) + Ntip
     }
-    if (node <= Ntip) stop("node number must be greater than the number of tips")
+    if (node <= Ntip)
+        stop("node number must be greater than the number of tips")
     if (node == ROOT) return(phy)
     phy <- reorder(phy) # insure it is in cladewise order
     root.node <- which(phy$edge[, 2] == node)
@@ -143,7 +144,7 @@ drop.tip <-
     ## 2) renumber the remaining tips now
     TIPS <- phy$edge[, 2] <= Ntip
     ## keep the ordering so no need to reorder tip.label:
-    phy$edge[TIPS, 2] <- order(phy$edge[TIPS, 2])
+    phy$edge[TIPS, 2] <- rank(phy$edge[TIPS, 2])
     Ntip <- length(phy$tip.label) # update Ntip
 
     ## make new tip labels if necessary
@@ -176,6 +177,6 @@ drop.tip <-
     phy$edge[sndcol, 2] <- newNb[phy$edge[sndcol, 2]] <-
         (Ntip + 2):(Ntip + phy$Nnode)
     phy$edge[, 1] <- newNb[phy$edge[, 1]]
-
+    storage.mode(phy$edge) <- "integer"
     collapse.singles(phy)
 }
diff --git a/man/plot.phylo.Rd b/man/plot.phylo.Rd
index b9622ef..dcabb28 100644
--- a/man/plot.phylo.Rd
+++ b/man/plot.phylo.Rd
@@ -184,16 +184,6 @@ plot(tree.owls, type = "c", use.edge.length = FALSE)
 plot(tree.owls, type = "u", use.edge.length = FALSE)
 layout(matrix(1))
 
-data(xenarthra)
-plot(xenarthra)
-### remove the margins...
-plot(xenarthra, no.margin = TRUE)
-### ... and use a smaller font size
-plot(xenarthra, no.margin = TRUE, cex = 0.8)
-plot(xenarthra, type = "c", no.margin = TRUE,
-     use.edge.length = FALSE, cex = 0.8)
-par(mar = c(5.1, 4.1, 4.1, 2.1))
-
 data(bird.orders)
 ### using random colours and thickness
 plot(bird.orders,
-- 
2.39.5