[Vegan-commits] r674 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-01-26 14:51:28 +0100 (Mon, 26 Jan 2009)
New Revision: 674

Modified:
   pkg/vegan/R/metaMDSdist.R
   pkg/vegan/inst/ChangeLog
Log:
metaMDSdist: do not evaluate no.shared() if set noshare=0


Modified: pkg/vegan/R/metaMDSdist.R
===================================================================
--- pkg/vegan/R/metaMDSdist.R	2009-01-26 13:31:00 UTC (rev 673)
+++ pkg/vegan/R/metaMDSdist.R	2009-01-26 13:51:28 UTC (rev 674)
@@ -37,13 +37,13 @@
         }
     }
     maxdis <- max(dis)
-    if (sum(tmp <- no.shared(comm))/length(dis) > noshare && noshare > 0) {
+    if (noshare > 0 && sum(tmp <- no.shared(comm))/length(dis) > noshare) {
         if (trace) 
             cat("Using step-across dissimilarities:\n")
         dis <- stepacross(dis, trace = trace, ...)
+        if (length(unique(distconnected(tmp, trace = trace > 1))) > 1) 
+            warning("Data are disconnected, results may be meaningless")
     }
-    if (length(unique(distconnected(tmp, trace = trace > 1))) > 1) 
-        warning("Data are disconnected, results may be meaningless")
     attr(dis, "maxdis") <- maxdis
     attr(dis, "commname") <- commname
     attr(dis, "function") <- distname

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-01-26 13:31:00 UTC (rev 673)
+++ pkg/vegan/inst/ChangeLog	2009-01-26 13:51:28 UTC (rev 674)
@@ -4,6 +4,9 @@
 
 Version 1.6-10 (openen Jan 20, 2009)
 
+	* metaMDS: really do not evaluate no.shared() if set
+	noshare=0. Triggered by a problem report with missing data. 
+
 	* vegdist doc: Morisita and Horn-Morisita were given as
 	similarities in the help.