[Vegan-commits] r735 - in pkg/vegan: . R inst

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

Author: jarioksa
Date: 2009-03-10 21:15:09 +0100 (Tue, 10 Mar 2009)
New Revision: 735

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/metaMDSdist.R
   pkg/vegan/inst/ChangeLog
Log:
metaMDS: automatic stepacross failed with Euclidean, Manhattan etc. distances

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2009-03-09 13:21:54 UTC (rev 734)
+++ pkg/vegan/DESCRIPTION	2009-03-10 20:15:09 UTC (rev 735)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.16-14
-Date: February 24, 2009
+Version: 1.16-15
+Date: March 10, 2009
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/vegan/R/metaMDSdist.R
===================================================================
--- pkg/vegan/R/metaMDSdist.R	2009-03-09 13:21:54 UTC (rev 734)
+++ pkg/vegan/R/metaMDSdist.R	2009-03-10 20:15:09 UTC (rev 735)
@@ -40,7 +40,8 @@
     if (noshare > 0 && sum(tmp <- no.shared(comm))/length(dis) > noshare) {
         if (trace) 
             cat("Using step-across dissimilarities:\n")
-        dis <- stepacross(dis, trace = trace, ...)
+        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: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-03-09 13:21:54 UTC (rev 734)
+++ pkg/vegan/inst/ChangeLog	2009-03-10 20:15:09 UTC (rev 735)
@@ -2,8 +2,14 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-14 (opened Feb 24, 2009)
+Version 1.16-15 (opened Mar 10, 2009)
 
+	* metaMDS: automatic stepacross works with Euclidean, Manhattan
+	and other distances with no fixed upper limit. Fixed after a query
+	to R-sig-ecology by Manuel Spinola.
+	
+Version 1.16-14 (closed Mar 10, 2009)
+
 	* as.mcmc.oecosimu: a new function to translate sequential null
 	models to "mcmc" object of the coda package. The coda package
 	provides a wealthy source of the analysis of things like