[Ecopd-commits] r84 - branches/single-tree/R

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

Author: regetz
Date: 2009-11-18 19:33:57 +0100 (Wed, 18 Nov 2009)
New Revision: 84

Modified:
   branches/single-tree/R/pd.R
Log:
superficial rearrangement of (temporary) error checking code in pd


Modified: branches/single-tree/R/pd.R
===================================================================
--- branches/single-tree/R/pd.R	2009-11-18 18:24:45 UTC (rev 83)
+++ branches/single-tree/R/pd.R	2009-11-18 18:33:57 UTC (rev 84)
@@ -28,11 +28,17 @@
 setMethod("pd", signature(x="phylo4com"), function(x,
   method=c("traditional", "polytomy", "yule")) {
 
+    method <- match.arg(method)
+
+    ##TODO fix abundance-weighted PD!
+    if (method %in% c("polytomy", "yule")) {
+        stop("Non-trad PD not yet implemented for phylo4com")
+    } 
+
     .pd <- function(phy, method) {
         ## if using non-traditional pd, adjust tip lengths based on abundance
         if (method %in% c("polytomy", "yule")) {
-            stop("Non-trad PD not yet implemented for phylo4com")
-#            phy <- weightByAbund(phy, method)
+            phy <- weightByAbund(phy, method)
         } 
         # exclude root edge from calculation (if it exists)
         if (isRooted(phy)) {
@@ -44,7 +50,6 @@
         return(tot.length)
     }
 
-    method <- match.arg(method)
     comms <- x at metadata$comms
     if (is.null(comms)) {
         return(.pd(extractTree(x), method))