fixes for ape 2.3-1

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@80 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/R/ltt.plot.R b/R/ltt.plot.R
index 15b53f8744e59dc8110f7bd3501f8bf8ea8998a4..a7eae04323169877a30c86b15984fa2256936e77 100644 (file)
--- 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 a191f9950cda149c73131433ec4edb62a52da4f0..b08446f6005a67dae11e2b9503a3f76bb14112e7 100644 (file)
--- 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 9c1f6dcf9da3a6073460fcc08e447a3f7ffb88a9..7e0c0c789355e857ee4c30a5b9ede04a26cca0cb 100644 (file)
--- 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 602f407b6e9489dcefc1e78f107bdba7eeb6b6bb..0206ccb24a653bb87c2ebc347f3735d28733d4a1 100644 (file)
--- 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 45aafe14808233674719a2c4efca38edeaae7627..5de597696182416dc2f7b72066fc59d6efbcf0f7 100644 (file)
--- 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 aedeef9699571b48a1d367ed2481862f5fa17f90..8b56c7ea3b050b2938cc048ba84d218fc7be70d2 100644 (file)
--- 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