[Adephylo-commits] r134 - pkg/man

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2009-11-05 14:21:48 +0100 (Thu, 05 Nov 2009)
New Revision: 134

Modified:
   pkg/man/adephylo.package.Rd
   pkg/man/distRoot.Rd
   pkg/man/distTips.Rd
   pkg/man/listDD.Rd
   pkg/man/listTips.Rd
   pkg/man/orthobasis.Rd
   pkg/man/orthogram.Rd
   pkg/man/proxTips.Rd
   pkg/man/sp.tips.Rd
   pkg/man/treePart.Rd
Log:
All seems to be fixed, no longer any warning.
Have to check examples now.


Modified: pkg/man/adephylo.package.Rd
===================================================================
--- pkg/man/adephylo.package.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/adephylo.package.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -12,7 +12,7 @@
 
   Comparative data (phylogeny+traits) are handled as
   \linkS4class{phylo4d} objects, a canonical class implemented by the
-  \code{phylobase} package. Trees are handled as \code{\link[ape]{phylo}}
+  \code{phylobase} package. Trees are handled as \code{\link[ape:read.tree]{phylo}}
   objects (from the \code{ape} package) or as \linkS4class{phylo4}
   objects (\code{phylobase}'s extension of \code{phylo} objects).\cr
 

Modified: pkg/man/distRoot.Rd
===================================================================
--- pkg/man/distRoot.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/distRoot.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -9,7 +9,7 @@
 distRoot(x, tips, method=c("patristic","nNodes","Abouheif","sumDD"))
 }
 \arguments{
-  \item{x}{a tree of  class \code{\link[ape]{phylo}},
+  \item{x}{a tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{tips}{A vector of integers identifying tips by their numbers, or
     a vector of characters identifying tips by their names.}

Modified: pkg/man/distTips.Rd
===================================================================
--- pkg/man/distTips.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/distTips.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -13,7 +13,7 @@
 distTips(x, tips, method=c("patristic","nNodes","Abouheif","sumDD"))
 }
 \arguments{
-  \item{x}{a tree of  class \code{\link[ape]{phylo}},
+  \item{x}{a tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{tips}{A vector of integers identifying tips by their numbers, or
     a vector of characters identifying tips by their names. Distances

Modified: pkg/man/listDD.Rd
===================================================================
--- pkg/man/listDD.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/listDD.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -3,14 +3,14 @@
 \title{List direct descendants for all nodes of a tree}
 \description{
   The function \code{listDD} lists the direct descendants from each node
-  of a tree. The tree can be of class \code{\link[ape]{phylo}},
+  of a tree. The tree can be of class \code{\link[ape:read.tree]{phylo}},
   \linkS4class{phylo4} or \linkS4class{phylo4d}.
 }
 \usage{
 listDD(x, nameBy=c("label","number"))
 }
 \arguments{
-  \item{x}{A tree of  class \code{\link[ape]{phylo}},
+  \item{x}{A tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{nameBy}{a character string indicating whether the returned list
     must be named by node labels ("label") or by node numbers ("number").}

Modified: pkg/man/listTips.Rd
===================================================================
--- pkg/man/listTips.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/listTips.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -3,14 +3,14 @@
 \title{List tips descendings from all nodes of a tree}
 \description{
   The function \code{listTips} lists the tips descending from each node
-  of a tree. The tree can be of class \code{\link[ape]{phylo}},
+  of a tree. The tree can be of class \code{\link[ape:read.tree]{phylo}},
   \linkS4class{phylo4} or \linkS4class{phylo4d}.
 }
 \usage{
 listTips(x)
 }
 \arguments{
-  \item{x}{A tree of  class \code{\link[ape]{phylo}},
+  \item{x}{A tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
 }
 \value{

Modified: pkg/man/orthobasis.Rd
===================================================================
--- pkg/man/orthobasis.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/orthobasis.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -25,7 +25,7 @@
 orthobasis.phylo(x=NULL, prox=NULL, method=c("patristic","nNodes","oriAbouheif","Abouheif","sumDD"), a=1)
 }
 \arguments{
-  \item{x}{A tree of  class \code{\link[ape]{phylo}},
+  \item{x}{A tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{prox}{a matrix of phylogenetic proximities as returned by \code{\link{proxTips}}.}
   \item{method}{a character string (full or abbreviated without

Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/orthogram.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -25,7 +25,7 @@
 }
 \arguments{
   \item{x}{a numeric vector corresponding to the quantitative variable}
-  \item{tre}{a tree of  class \code{\link[ape]{phylo}},
+  \item{tre}{a tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{orthobas}{an object of class \code{'orthobasis'}}
   \item{prox}{a matrix of phylogenetic proximities as returned by \code{\link{proxTips}}.}

Modified: pkg/man/proxTips.Rd
===================================================================
--- pkg/man/proxTips.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/proxTips.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -40,7 +40,7 @@
          a=1, normalize=c("row","col","none"), symmetric=TRUE)
 }
 \arguments{
-  \item{x}{a tree of  class \code{\link[ape]{phylo}},
+  \item{x}{a tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{tips}{A vector of integers identifying tips by their numbers, or
     a vector of characters identifying tips by their names. Distances

Modified: pkg/man/sp.tips.Rd
===================================================================
--- pkg/man/sp.tips.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/sp.tips.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -4,14 +4,14 @@
 \description{
   The function \code{sp.tips} finds the shortest path between tips of a
   tree, identified as \code{tip1} and \code{tip2}.
-  This function applies to trees with the class \code{\link[ape]{phylo}}, \linkS4class{phylo4} or
+  This function applies to trees with the class \code{\link[ape:read.tree]{phylo}}, \linkS4class{phylo4} or
   \linkS4class{phylo4d}. Several tips can be provided at a time.
 }
 \usage{
 sp.tips(x, tip1, tip2, useTipNames=FALSE, quiet=FALSE, include.mrca=TRUE)
 }
 \arguments{
-  \item{x}{A tree of  class \code{\link[ape]{phylo}},
+  \item{x}{A tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{tip1}{A vector of integers identifying tips by their numbers, or
     a vector of characters identifying tips by their names. Recycled if needed.}

Modified: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd	2009-11-05 13:12:12 UTC (rev 133)
+++ pkg/man/treePart.Rd	2009-11-05 13:21:48 UTC (rev 134)
@@ -16,7 +16,7 @@
 treePart(x, result=c("dummy", "orthobasis"))
 }
 \arguments{
-  \item{x}{a tree of  class \code{\link[ape]{phylo}},
+  \item{x}{a tree of  class \code{\link[ape:read.tree]{phylo}},
     \linkS4class{phylo4} or \linkS4class{phylo4d}.}
   \item{result}{a character string specifying the type of result: either
   a basis of dummy vectors (\code{dummy}), or an orthobasis derived from these dummy vectors (\code{orthobasis}).}