[Mattice-commits] r53 - pkg/R

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

Author: amesclir
Date: 2008-11-24 19:51:03 +0100 (Mon, 24 Nov 2008)
New Revision: 53

Modified:
   pkg/R/regimes.R
Log:
Got rid of tree checking block at the beginning of regimes.R... don?\194?\180t know why it was still there, not needed

Modified: pkg/R/regimes.R
===================================================================
--- pkg/R/regimes.R	2008-11-21 17:37:46 UTC (rev 52)
+++ pkg/R/regimes.R	2008-11-24 18:51:03 UTC (rev 53)
@@ -19,17 +19,6 @@
 #  "nodeMatrix" = matrix of trees (rows) by nodes (columns) indicating what nodes are present on which trees
 # 19 nov 08: changing to accept a list of trees and trimmed down greatly
 function(ouchTrees, cladeMembersList, maxNodes = NULL) {
-  ## ------------------ begin ouchtree block -----------------
-  ## check to see if tree inherits 'ouchtree'
-  if (!is(tree,'ouchtree')) 
-	stop(paste('This function has been rewritten to use the new S4 ', sQuote('ouchtree'), ' class.',
-	'\nYou can generate a tree of this class by calling ', sQuote('ouchtree()'), '.', sep = ""))
-  ## get the vectors we need:
-  ancestor <- tree at ancestors # class = "character"
-  node <- tree at nodes # class = "character"
-  species <- tree at nodelabels # class = "character" -- note that nodelabels is more general than this indicates and the name should be changed throughout at some point
-  times <- tree at times # class = "numeric"
-  ## ------------------ end ouchtree block -------------------
   
   nnode <- length(cladeMembersList)
   regMatrix <- regimeMatrix(n = nnode, maxNodes = maxNodes)