[Phylobase-commits] r325 - pkg/R

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

Author: francois
Date: 2008-12-19 13:52:47 +0100 (Fri, 19 Dec 2008)
New Revision: 325

Modified:
   pkg/R/methods-phylo4.R
Log:
nTips now returns 0 on empty trees

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2008-12-19 10:51:53 UTC (rev 324)
+++ pkg/R/methods-phylo4.R	2008-12-19 12:52:47 UTC (rev 325)
@@ -7,12 +7,16 @@
 
 setMethod("nTips", "phylo4", function(x, ...) {
     E <- edges(x)
-    ## doesn't handle reticulated networks
-    ##    res <- sum(!E[, 2] %in% E[, 1])
-    res <- sum(tabulate(E[,1]) == 0) ## twice as fast as ...
-    ## change suggested by Aaron Mackey, handles reticulated networks better
-    ## res <- sum(!(unique(E[,2]) %in% E[,1]))
-    return(res)
+    if(nrow(E) == 0)
+        return(0)
+    else {
+        ## doesn't handle reticulated networks
+        ##    res <- sum(!E[, 2] %in% E[, 1])
+        res <- sum(tabulate(E[,1]) == 0) ## twice as fast as ...
+        ## change suggested by Aaron Mackey, handles reticulated networks better
+        ## res <- sum(!(unique(E[,2]) %in% E[,1]))
+        return(res)
+    }
 })
 
 ## hack to ensure ape compatibility
@@ -47,9 +51,9 @@
     ## HACK: make sure we find the right "nTips"
     tabulate(edges(x)[, 1])[nTips(x) + 1] <= 2
     ## root node (first node after last tip) has <= 2 descendants
-    ## FIXME (?): fails with empty tree
 })
 
+
 setMethod("rootNode", "phylo4", function(x) {
     if (!isRooted(x))
         return(NA)