[Phylobase-commits] r641 - pkg/man

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

Author: pdc
Date: 2009-09-12 03:20:06 +0200 (Sat, 12 Sep 2009)
New Revision: 641

Modified:
   pkg/man/phylo4-accessors.Rd
   pkg/man/phylo4-labels.Rd
   pkg/man/treewalk.Rd
Log:
Change docs to reflect new method argument names

Modified: pkg/man/phylo4-accessors.Rd
===================================================================
--- pkg/man/phylo4-accessors.Rd	2009-09-12 01:01:42 UTC (rev 640)
+++ pkg/man/phylo4-accessors.Rd	2009-09-12 01:20:06 UTC (rev 641)
@@ -77,14 +77,14 @@
 % what a pain: see
 % https://stat.ethz.ch/pipermail/r-devel/2008-May/049653.html
 \S4method{nNodes}{phylo4}(x)
-\S4method{nTips}{phylo4}(x, \dots)
+\S4method{nTips}{phylo4}(x)
 \S4method{edges}{phylo4}(x, order, drop.root=FALSE, \dots)
 \S4method{nEdges}{phylo4}(x)
 \S4method{edgeOrder}{phylo4}(x, \dots)
 \S4method{hasEdgeLength}{phylo4}(x)
 \S4method{edgeLength}{phylo4}(x, node)
 \S4method{edgeLength}{phylo4}(x, use.names=TRUE) <- value
-\S4method{nodeType}{phylo4}(phy)
+\S4method{nodeType}{phylo4}(x)
 \S4method{isRooted}{phylo4}(x)
 \S4method{rootEdge}{phylo4}(x)
 \S4method{rootNode}{phylo4}(x)
@@ -93,7 +93,6 @@
 
 \arguments{
   \item{x}{a phylo4/phylo4d object}
-  \item{phy}{a phylo4/phylo4d object}
   \item{node}{which edge lengths to extract (indexed by descendant
     node)} 
   \item{value}{a vector of edge lengths or a node number}

Modified: pkg/man/phylo4-labels.Rd
===================================================================
--- pkg/man/phylo4-labels.Rd	2009-09-12 01:01:42 UTC (rev 640)
+++ pkg/man/phylo4-labels.Rd	2009-09-12 01:20:06 UTC (rev 641)
@@ -1,4 +1,4 @@
-\name{labels-phylo4}
+\name{phylo4-labels}
 \docType{methods}
 \alias{labels<-}
 \alias{labels,phylo4-method}
@@ -35,16 +35,16 @@
 
 \usage{
 
-\S4method{labels}{phylo4}(object, type=c("all", "tip", "internal"), \dots)
+\S4method{labels}{phylo4}(object, type=c("all", "tip", "internal"))
 \S4method{labels}{phylo4,ANY,ANY,character}(x, type=c("tip", "internal", "allnode"),
 use.names=FALSE) <- value
 
-\S4method{tipLabels}{phylo4}(object)
-\S4method{tipLabels}{phylo4,character}(object) <- value
+\S4method{tipLabels}{phylo4}(x)
+\S4method{tipLabels}{phylo4,character}(x) <- value
 
 \S4method{hasNodeLabels}{phylo4}(x)
-\S4method{nodeLabels}{phylo4}(object)
-\S4method{nodeLabels}{phylo4,character}(object) <- value
+\S4method{nodeLabels}{phylo4}(x)
+\S4method{nodeLabels}{phylo4,character}(x) <- value
 
 \S4method{hasEdgeLabels}{phylo4}(x)
 \S4method{edgeLabels}{phylo4}(x)
@@ -61,7 +61,6 @@
     information.}
   \item{use.names}{should the names of the vector used to create/update
     labels be used to match the labels? See Details for more information.}
-  \item{\dots}{additional parameter passed to the function (currently ignored)}
 }
 
 \details{

Modified: pkg/man/treewalk.Rd
===================================================================
--- pkg/man/treewalk.Rd	2009-09-12 01:01:42 UTC (rev 640)
+++ pkg/man/treewalk.Rd	2009-09-12 01:20:06 UTC (rev 641)
@@ -28,12 +28,15 @@
 descendants(phy, node, type=c("tips","children","all"))
 MRCA(phy,\dots)
 shortestPath(phy, node1, node2)
-\S4method{sumEdgeLength}{phylo4}(phy, node)
+\S4method{sumEdgeLength}{phylo4}(x, node)
 }
 \arguments{
   \item{phy}{a \linkS4class{phylo4} object (or one inheriting from
     \linkS4class{phylo4}, e.g. a \linkS4class{phylo4d} object)
   }
+  \item{x}{a \linkS4class{phylo4} object (or one inheriting from
+    \linkS4class{phylo4}, e.g. a \linkS4class{phylo4d} object)
+  }
   \item{node}{a node ID number (or name)}
   \item{type}{(\code{ancestors}) specify whether to return just direct
     ancestor ("parent"), all ancestor nodes ("all"), or all ancestor