[Phylobase-commits] r499 - pkg/man

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

Author: pdc
Date: 2009-08-19 02:59:35 +0200 (Wed, 19 Aug 2009)
New Revision: 499

Modified:
   pkg/man/subset-methods.Rd
Log:
A bit over ambitious w/ the delete, restoring some arguments that did actually exist in the code

Modified: pkg/man/subset-methods.Rd
===================================================================
--- pkg/man/subset-methods.Rd	2009-08-19 00:50:25 UTC (rev 498)
+++ pkg/man/subset-methods.Rd	2009-08-19 00:59:35 UTC (rev 499)
@@ -33,14 +33,17 @@
   Renamed from \code{drop.tip} to \code{prune} in order to
   avoid conflicts with ape.}
 \usage{
-\S4method{subset}{phylo4}(x, \dots)
+\S4method{subset}{phylo4}(x, tips.include=NULL, tips.exclude=NULL, mrca=NULL, node.subtree=NULL, \dots)
 
-\S4method{subset}{phylo4d}(x, \dots)
-
+\S4method{subset}{phylo4d}(x, tips.include=NULL, tips.exclude=NULL, mrca=NULL, node.subtree=NULL, \dots)
 \S4method{subset}{phylo}(x, \dots)
 }
 \arguments{
   \item{x}{an object of class \code{"phylo4"}, \code{"phylo"} or \code{"phylo4d"}}
+  \item{tips.include}{A vector containing tips to include in the pruned tree}
+  \item{tips.exclude}{A vector containing tips to exclude from the pruned tree}
+  \item{mrca}{Prune tree to include all descendants of the most recent common ancestor of the specified taxa}
+  \item{node.subtree}{Prune to all descendants of a specified node}
   \item{\dots}{further arguments to be passed to other methods}
 }
 \details{