From 4764f968dcbb65566d8196c154179d629da79fb2 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Tue, 23 Jun 2009 13:39:20 +0000
Subject: [PATCH] fixes for ape 2.3-1

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@80 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 R/ltt.plot.R              | 2 +-
 man/DNAbin.Rd             | 1 +
 man/Initialize.corPhyl.Rd | 2 +-
 man/ape-internal.Rd       | 1 +
 man/is.monophyletic.Rd    | 2 +-
 man/opsin.Rd              | 3 ---
 6 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/R/ltt.plot.R b/R/ltt.plot.R
index 15b53f8..a7eae04 100644
--- a/R/ltt.plot.R
+++ b/R/ltt.plot.R
@@ -35,7 +35,7 @@ mltt.plot <- function(phy, ..., dcol = TRUE, dlty = FALSE, legend = TRUE,
         y <- 1:length(x)
         cbind(x, y)
     }
-    if if (inherits(phy, "phylo")) { # if a tree of class "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
diff --git a/man/DNAbin.Rd b/man/DNAbin.Rd
index a191f99..b08446f 100644
--- a/man/DNAbin.Rd
+++ b/man/DNAbin.Rd
@@ -6,6 +6,7 @@
 \alias{rbind.DNAbin}
 \alias{cbind.DNAbin}
 \alias{as.matrix.DNAbin}
+\alias{c.DNAbin}
 \title{Manipulate DNA Sequences in Bit-Level Format}
 \description{
   These functions help to manipulate DNA sequences coded in the
diff --git a/man/Initialize.corPhyl.Rd b/man/Initialize.corPhyl.Rd
index 9c1f6dc..7e0c0c7 100644
--- a/man/Initialize.corPhyl.Rd
+++ b/man/Initialize.corPhyl.Rd
@@ -1,6 +1,6 @@
 \name{Initialize.corPhyl}
 \alias{Initialize.corPhyl}
-\title{Initialize a 'corPhyl' Structure Object}
+\title{Initialize a `corPhyl' Structure Object}
 \usage{
 	\method{Initialize}{corPhyl}(object, data, ...)
 }
diff --git a/man/ape-internal.Rd b/man/ape-internal.Rd
index 602f407..0206ccb 100644
--- a/man/ape-internal.Rd
+++ b/man/ape-internal.Rd
@@ -1,4 +1,5 @@
 \name{ape-internal}
+\alias{klastorin}
 \alias{tree.build}
 \alias{f.cherry.yule}
 \alias{f.cherry.uniform}
diff --git a/man/is.monophyletic.Rd b/man/is.monophyletic.Rd
index 45aafe1..5de5976 100644
--- a/man/is.monophyletic.Rd
+++ b/man/is.monophyletic.Rd
@@ -4,7 +4,7 @@
   Is Group Monophyletic
 }
 \usage{
-is.monophyletic(phy, tips, reroot = NULL, plot = FALSE, ...)
+is.monophyletic(phy, tips, reroot = !is.rooted(phy), plot = FALSE, ...)
 }
 \description{
     This function tests whether a list of tip labels is monophyletic on a given tree.
diff --git a/man/opsin.Rd b/man/opsin.Rd
index aedeef9..8b56c7e 100644
--- a/man/opsin.Rd
+++ b/man/opsin.Rd
@@ -16,9 +16,6 @@ data(opsin.newick)
   This tree is described in Misawa and Tajima (2000) as an example
   for application of the Klastorin (1982) classification method.
 }
-\seealso{
-\code{\link{klastorin}}.
-}
 \references{
   Misawa, K. (2000) A simple method for classifying genes and a bootstrap
   test for classifications. \emph{Molecular
-- 
2.39.2