[Phylobase-commits] r475 - in pkg: . R

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

Author: bbolker
Date: 2009-08-18 20:31:08 +0200 (Tue, 18 Aug 2009)
New Revision: 475

Removed:
   pkg/R/updatePhylo4.R
Modified:
   pkg/DESCRIPTION
Log:
 removed updatePhylo4



Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2009-08-18 18:21:25 UTC (rev 474)
+++ pkg/DESCRIPTION	2009-08-18 18:31:08 UTC (rev 475)
@@ -9,6 +9,6 @@
 Maintainer:  Ben Bolker <bolker at ufl.edu>
 Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data
 License: GPL
-Collate: phylo4.R checkdata.R class-multiphylo4.R class-oldclasses.R class-phylo4.R class-phylo4d.R  class-phylomats.R methods-multiphylo4.R methods-oldclasses.R methods-phylo4.R methods-phylo4d.R setAs-Methods.R pdata.R subset.R prune.R treePlot.R identify.R treestruc.R treewalk.R readNexus.R tbind.R zzz.R printphylo-deprecated.R updatePhylo4.R 
+Collate: phylo4.R checkdata.R class-multiphylo4.R class-oldclasses.R class-phylo4.R class-phylo4d.R  class-phylomats.R methods-multiphylo4.R methods-oldclasses.R methods-phylo4.R methods-phylo4d.R setAs-Methods.R pdata.R subset.R prune.R treePlot.R identify.R treestruc.R treewalk.R readNexus.R tbind.R zzz.R printphylo-deprecated.R 
 Encoding: UTF-8
 URL: http://phylobase.R-forge.R-project.org

Deleted: pkg/R/updatePhylo4.R
===================================================================
--- pkg/R/updatePhylo4.R	2009-08-18 18:21:25 UTC (rev 474)
+++ pkg/R/updatePhylo4.R	2009-08-18 18:31:08 UTC (rev 475)
@@ -1,26 +0,0 @@
-updatePhylo4 <- function(phy, ...) {
-    ## Add internal names for tip labels
-    if(is.null(names(phy at tip.label))) {
-        if(length(phy at tip.label == nTips(phy))) {
-            names(phy at tip.label) <- nodeId(phy, "tip")
-        }
-        else stop("You have a problem with your tip labels")
-    }
-
-    ## Add internal names for node labels
-    if(is.null(names(phy at node.label))) {
-        if(length(phy at node.label) == nNodes(phy)) {
-            names(phy at node.label) <- nodeId(phy, "internal")
-        }
-        else stop("You have a problem with your node labels.")
-    }
-
-    ## Add internal names for edge lengths
-    if(hasEdgeLength(phy) && is.null(names(phy at edge.length))) {
-        names(phy at edge.length) <- paste(phy at edge[,1], phy at edge[,2], sep="-")
-    }
-
-    if(is.character(msg <- checkPhylo4(phy))) stop(msg)
-    else return(phy)
-
-}