[Phylobase-commits] r581 - in pkg: . man

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

Author: regetz
Date: 2009-08-25 01:26:23 +0200 (Tue, 25 Aug 2009)
New Revision: 581

Modified:
   pkg/NAMESPACE
   pkg/man/phylo4-class.Rd
   pkg/man/phylo4.Rd
   pkg/man/phylo4d-class.Rd
Log:
fixed documentation about allowable values of phylo4 'order'; also added
phylo4_orderings to the NAMESPACE file


Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2009-08-24 23:11:24 UTC (rev 580)
+++ pkg/NAMESPACE	2009-08-24 23:26:23 UTC (rev 581)
@@ -75,6 +75,11 @@
 export(as_phylo4vcov)
 export(printphylo4)
 
+#----------------------------------------------------------------------
+
+# misc objects
+export(phylo4_orderings)
+
 ## commented out in source code, probably should be omitted here
 #export(phyloStripchart)
 #export(internEdges, terminEdges, isPoly)

Modified: pkg/man/phylo4-class.Rd
===================================================================
--- pkg/man/phylo4-class.Rd	2009-08-24 23:11:24 UTC (rev 580)
+++ pkg/man/phylo4-class.Rd	2009-08-24 23:26:23 UTC (rev 581)
@@ -24,9 +24,10 @@
     \item{\code{tip.label}:}{character vector of tip labels}
     \item{\code{root.edge}:}{integer: root edge (NA if none)}
     \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} }
+      listed in \code{phylo4_orderings}, currently "unknown", "preorder"
+      (="cladewise" in \code{ape}), and "postorder", with "cladewise"
+      and "pruningwise" also allowed for compatibility with \code{ape})} }
   }
-  }
 \section{Methods}{
   \describe{
     \item{\$}{\code{signature(x = "phylo4")}: extract a slot}

Modified: pkg/man/phylo4.Rd
===================================================================
--- pkg/man/phylo4.Rd	2009-08-24 23:11:24 UTC (rev 580)
+++ pkg/man/phylo4.Rd	2009-08-24 23:26:23 UTC (rev 581)
@@ -30,9 +30,9 @@
   \item{node.label}{A character vector of internal node names. (Optional)}
   \item{edge.label}{A character vector of edge (branch) names. (Optional)}
   \item{order}{character: tree ordering (allowable values are
-      listed in \code{phylo4_ordering}, currently "unknown", "reorder"
-      (="pruningwise" in \code{ape}), "postorder" (="cladewise" in
-      \code{ape}))}
+      listed in \code{phylo4_orderings}, currently "unknown", "preorder"
+      (="cladewise" in \code{ape}), and "postorder", with "cladewise"
+      and "pruningwise" also allowed for compatibility with \code{ape})}
   \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.}

Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd	2009-08-24 23:11:24 UTC (rev 580)
+++ pkg/man/phylo4d-class.Rd	2009-08-24 23:26:23 UTC (rev 581)
@@ -28,7 +28,10 @@
     \item{\code{tip.label}:}{Character vector of tip labels}
     % \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})}
+    \item{\code{order}:}{character: tree ordering (allowable values are
+      listed in \code{phylo4_orderings}, currently "unknown", "preorder"
+      (="cladewise" in \code{ape}), and "postorder", with "cladewise"
+      and "pruningwise" also allowed for compatibility with \code{ape})}
   }
 }
 \section{Methods}{