[Phylobase-commits] r390 - pkg/R

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

Author: bbolker
Date: 2008-12-22 03:30:59 +0100 (Mon, 22 Dec 2008)
New Revision: 390

Modified:
   pkg/R/checkdata.R
Log:
  test for negative edge lengths



Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R	2008-12-21 23:47:12 UTC (rev 389)
+++ pkg/R/checkdata.R	2008-12-22 02:30:59 UTC (rev 390)
@@ -7,8 +7,12 @@
 check_tree <- function(object,warn="retic",err=NULL) {
     ## FIXME: check for cyclicity?
     nedges <- nrow(object at edge)
-    if (hasEdgeLength(object) && length(object at edge.length) != nedges)
-      return("edge lengths do not match number of edges")
+    if (hasEdgeLength(object)) {
+      if (length(object at edge.length) != nedges)
+        return("edge lengths do not match number of edges")
+      if (any(object at edge.length<0))
+        return("edge lengths must be non-negative")
+    }
     ## if (length(object at tip.label)+object at Nnode-1 != N) # does not work with multifurcations
     ##  return("number of tip labels not consistent with number of edges and nodes")
     ## check: tip numbers = (m+1):(m+n)