[Vegan-commits] r1302 - pkg/vegan/R

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

Author: jarioksa
Date: 2010-09-13 22:11:48 +0200 (Mon, 13 Sep 2010)
New Revision: 1302

Modified:
   pkg/vegan/R/metaMDSdist.R
Log:
tweaking with NA distances and messages

Modified: pkg/vegan/R/metaMDSdist.R
===================================================================
--- pkg/vegan/R/metaMDSdist.R	2010-09-13 19:47:05 UTC (rev 1301)
+++ pkg/vegan/R/metaMDSdist.R	2010-09-13 20:11:48 UTC (rev 1302)
@@ -32,13 +32,13 @@
     call <- attr(dis, "call")
     call[[1]] <- as.name(distname)
     attr(dis, "call") <- call
-    if (any(dis <= 0)) {
+    if (any(dis <= 0, na.rm = TRUE)) {
         if (zerodist == "fail") 
             stop("Zero dissimilarities are not allowed")
         else if (zerodist == "add") {
             zero <- min(dis[dis > 0], na.rm = TRUE)/2
             dis[dis <= 0] <- zero
-            warning("Zero dissimilarities changed into ", zero)
+            message("Zero dissimilarities changed into ", zero)
         }
     }
     ## We actually used maxdis to decide whether index has a closed