[Vegan-commits] r737 - in branches/1.15: R inst

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

Author: jarioksa
Date: 2009-03-11 18:24:00 +0100 (Wed, 11 Mar 2009)
New Revision: 737

Modified:
   branches/1.15/R/metaMDSdist.R
   branches/1.15/inst/ChangeLog
Log:
merged r735 & 736 to the 1.15-2: stepacross in metaMDS fixes for Euclidean etc. distances

Modified: branches/1.15/R/metaMDSdist.R
===================================================================
--- branches/1.15/R/metaMDSdist.R	2009-03-11 17:13:38 UTC (rev 736)
+++ branches/1.15/R/metaMDSdist.R	2009-03-11 17:24:00 UTC (rev 737)
@@ -40,7 +40,12 @@
     if (sum(tmp <- no.shared(comm))/length(dis) > noshare && noshare > 0) {
         if (trace) 
             cat("Using step-across dissimilarities:\n")
-        dis <- stepacross(dis, trace = trace, ...)
+        rn <- range(dis[tmp])
+        if (rn[2]/rn[1] > 1.01)
+            warning("non-constant distances between points with nothing shared\n",
+                    "  stepacross may be meaningless: consider argument 'noshare=0'")
+        is.na(dis) <- tmp
+        dis <- stepacross(dis, trace = trace, toolong=0, ...)
     }
     if (length(unique(distconnected(tmp, trace = trace > 1))) > 1) 
         warning("Data are disconnected, results may be meaningless")

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-03-11 17:13:38 UTC (rev 736)
+++ branches/1.15/inst/ChangeLog	2009-03-11 17:24:00 UTC (rev 737)
@@ -5,6 +5,9 @@
 
 Version 1.15-2 (opened January 14, 2009)
 
+	* merged r735 & r736: stepacross fixes in metaMDSdist with
+	open-ended dissimilarities (Euclidean, Manhattan etc.).
+
 	* merged r728: oecosimu.Rd example knows "statistic" argument.
 	
 	* merged r683 & r690: anova.cca(..., by = "margin") gained