[Vegan-commits] r2004 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-11-16 09:21:44 +0100 (Wed, 16 Nov 2011)
New Revision: 2004

Modified:
   pkg/vegan/R/metaMDSdist.R
   pkg/vegan/inst/ChangeLog
Log:
metaMDS(..., noshare = 0) will always trigger stepcaross() and 'noshare = FALSE' will never do so

Modified: pkg/vegan/R/metaMDSdist.R
===================================================================
--- pkg/vegan/R/metaMDSdist.R	2011-11-15 09:24:20 UTC (rev 2003)
+++ pkg/vegan/R/metaMDSdist.R	2011-11-16 08:21:44 UTC (rev 2004)
@@ -49,7 +49,7 @@
     maxdis <- abs(distfun(matrix(c(7,0,0,3), 2, 2),
                       method = distance, ...) - 1) < 1e-4
     if ((isTRUE(noshare) && any(tmp <- no.shared(comm))) ||
-        (noshare > 0 &&
+        (!is.logical(noshare) && noshare >= 0 &&
          sum(tmp <- no.shared(comm))/length(dis) > noshare)) {
         if (trace) 
             cat("Using step-across dissimilarities:\n")

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-11-15 09:24:20 UTC (rev 2003)
+++ pkg/vegan/inst/ChangeLog	2011-11-16 08:21:44 UTC (rev 2004)
@@ -8,6 +8,11 @@
 	transposed matrices to internal f.test function. Reported by
 	Nicholas Lewin-Koh.
 
+	* metaMDS: arguments 'noshare = 0' and 'noshare = FALSE' are now
+	different: zero is taken as the numeric threshold and always
+	triggers stepacross(), whereas FALSE is logical and never triggers
+	stepacross.
+
 Version 2.1-6 (closed November 12, 2011)
 
 	* FAQ: correct mark-up of hyper links (@uref{} instead of @url{}),