[Phylobase-commits] r503 - pkg/man

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

Author: bbolker
Date: 2009-08-19 17:16:15 +0200 (Wed, 19 Aug 2009)
New Revision: 503

Modified:
   pkg/man/check.phylo4.Rd
   pkg/man/phylo4d-class.Rd
   pkg/man/phylo4d.Rd
Log:
  doc tweaks to fix 2.10.0 warnings



Modified: pkg/man/check.phylo4.Rd
===================================================================
--- pkg/man/check.phylo4.Rd	2009-08-19 07:13:42 UTC (rev 502)
+++ pkg/man/check.phylo4.Rd	2009-08-19 15:16:15 UTC (rev 503)
@@ -16,7 +16,7 @@
   \item{err}{a character vector listing phenomena to trigger errors}
 }
 \value{
-  As required by \code{\link{validObject}}, returns an
+  As required by \code{\link[methods]{validObject}}, returns an
   error string (describing problems) or TRUE if everything is OK
 }
 \note{\code{checkPhylo4} is an (inflexible) wrapper for

Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd	2009-08-19 07:13:42 UTC (rev 502)
+++ pkg/man/phylo4d-class.Rd	2009-08-19 15:16:15 UTC (rev 503)
@@ -19,14 +19,16 @@
 \section{Slots}{
   \describe{
     \item{\code{edge}:}{Matrix of edges}
-    \item{\code{edge.length}:}{Numeric vector of edge lengths}
+    \item{\code{edge.label}:}{Character vector of edge (branch) labels}
+    \item{\code{edge.length}:}{Numeric vector of edge (branch) lengths}
     \item{\code{Nnode}:}{Integer: number of nodes}
+    \item{\code{node.data}:}{data frame for traits of internal
+      nodes}
+    \item{\code{node.label}:}{Character vector of node labels}
     \item{\code{tip.label}:}{Character vector of tip labels}
-    \item{\code{root.edge}:}{Integer: root edge (NA if none)}
-    \item{\code{tipdata}:}{data frame for traits of tips}
-    \item{\code{nodedata}:}{data frame for traits of internal
-      nodes}
-    \item{\code{edgedata}:}{data frame for traits of edges}
+    % \item{\code{root.edge}:}{Integer: root edge (NA if none)}
+    \item{\code{tip.data}:}{data frame for traits of tips}
+    \item{\code{order}:}{character: tree ordering (allowable values are listed in \code{phylo4_orderings}, currently "unknown", "preorder", "postorder" (="cladewise" in \code{ape})), ("pruningwise" and "cladewise" are allowed for compatibility with \code{ape})}
   }
 }
 \section{Methods}{
@@ -39,8 +41,8 @@
     \item{head}{\code{signature(object = "phylo4d")}: show first few
 nodes}
     \item{tail}{\code{signature(object = "phylo4d")}: show last few nodes}
+  }
 }
-}
 \usage{
     \S4method{print}{phylo4d}(x, printall=TRUE)
     \S4method{summary}{phylo4d}(object)

Modified: pkg/man/phylo4d.Rd
===================================================================
--- pkg/man/phylo4d.Rd	2009-08-19 07:13:42 UTC (rev 502)
+++ pkg/man/phylo4d.Rd	2009-08-19 15:16:15 UTC (rev 503)
@@ -14,11 +14,9 @@
   \describe{
      \item{x = "phylo4"}{merges a tree of class \code{phylo4} with a
        data.frame into a \code{phylo4d} object}
-
      \item{x = "matrix"}{merges a matrix of tree edges similar to the edge
        slot of a \code{phylo4} object (or to \$edge of a \code{phylo} object) with a
        data.frame into a \code{phylo4d} object}
-
      \item{x = "phylo"}{merges a tree of class \code{phylo} with a
        data.frame into a \code{phylo4d} object }
    }}