[Phylobase-commits] r496 - pkg/man

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

Author: pdc
Date: 2009-08-19 02:47:53 +0200 (Wed, 19 Aug 2009)
New Revision: 496

Modified:
   pkg/man/phylo4.Rd
   pkg/man/phylo4d.Rd
Log:
More methods documentation updates 


Modified: pkg/man/phylo4.Rd
===================================================================
--- pkg/man/phylo4.Rd	2009-08-19 00:45:10 UTC (rev 495)
+++ pkg/man/phylo4.Rd	2009-08-19 00:47:53 UTC (rev 496)
@@ -19,7 +19,7 @@
 \usage{
      \S4method{phylo4}{matrix}(x, edge.length = NULL, tip.label = NULL, node.label = NULL,
         edge.label = NULL,  order="unknown", ...)
-     \S4method{phylo4}{phylo}(x, check.node.labels = c("keep", "drop"), ...)
+     \S4method{phylo4}{phylo}(x, check.node.labels = c("keep", "drop"))
 }
 \arguments{
   \item{x}{a matrix of edges or an object of class \code{phylo} (see
@@ -36,7 +36,6 @@
   \item{check.node.labels}{if \code{x} is of class \code{phylo}, either
     "keep" (the default) or "drop" node labels. This argument is useful
     if the \code{phylo} object has non-unique node labels.}
-  \item{\dots}{fixme?}
 }
 \details{
   The minimum information necessary to create a phylobase tree object is a valid edge matrix. The edge matrix describes the topology of the phylogeny. Each row describes a branch of the phylogeny, with the (descendant) node number in column 2 and its ancestor's node number in column 1. These numbers are used internally and must be unique for each node.

Modified: pkg/man/phylo4d.Rd
===================================================================
--- pkg/man/phylo4d.Rd	2009-08-19 00:45:10 UTC (rev 495)
+++ pkg/man/phylo4d.Rd	2009-08-19 00:47:53 UTC (rev 496)
@@ -25,12 +25,11 @@
 
 \usage{
      \S4method{phylo4d}{phylo4}(x, tip.data = NULL, node.data = NULL,
-        all.data = NULL, merge.tip.node = TRUE, ...)
+        all.data = NULL, match.data = TRUE, merge.data = TRUE, ...)
      \S4method{phylo4d}{phylo}(x, tip.data = NULL, node.data = NULL,
-        all.data = NULL, merge.tip.node = TRUE,
-        check.node.labels = c("keep", "drop", "asdata"), ...)
+        all.data = NULL, check.node.labels = c("keep", "drop", "asdata"), ...)
      \S4method{phylo4d}{matrix}(x, tip.data = NULL, node.data = NULL,
-        all.data = NULL, merge.tip.node = TRUE, ...)
+        all.data = NULL, ...)
 }
 
 \arguments{
@@ -40,7 +39,8 @@
   \item{node.data}{a data frame for nodes data}
   \item{all.data}{a data frame for all (i.e. tips and nodes) data. In such
     case, first rows should correspond to tips, last rows to nodes.}
-  \item{merge.tip.node}{if both \code{tip.data} and \code{node.data} are
+  \item{match.data}{FIXME}
+  \item{merge.data}{if both \code{tip.data} and \code{node.data} are
     provided, it determines if they should be merged as a single
     trait. This argument is evaluated only if both \code{tip.data} and
     \code{node.data} have identical column names.}