[Vegan-commits] r762 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-03-26 23:12:04 +0100 (Thu, 26 Mar 2009)
New Revision: 762

Modified:
   pkg/vegan/R/postMDS.R
   pkg/vegan/inst/ChangeLog
Log:
postMDS: if halfchange = FALSE, scale max ordination distance equal to max input dissimilarity

Modified: pkg/vegan/R/postMDS.R
===================================================================
--- pkg/vegan/R/postMDS.R	2009-03-26 09:52:59 UTC (rev 761)
+++ pkg/vegan/R/postMDS.R	2009-03-26 22:12:04 UTC (rev 762)
@@ -27,6 +27,9 @@
             hc <- (1 - k[1])/2/k[2]
             x <- x/hc
         }
+    } else {
+        scl <- max(dist)/max(vegdist(x, "euclidean"))
+        x <- x*scl
     }
     if (plot && halfchange) {
         cross.lim <- 45

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-03-26 09:52:59 UTC (rev 761)
+++ pkg/vegan/inst/ChangeLog	2009-03-26 22:12:04 UTC (rev 762)
@@ -4,6 +4,10 @@
 
 Version 1.16-16 (openen Mar 25, 2009)
 
+	* metaMDS: scale ordination scores to the same max distance as
+	input dissimilarities if halfchange = FALSE (not yet documented,
+	still experimental).
+
 	* mrpp: reports now "classification strength" when weight.type = 3
 	or weights n*(n-1) are used. Returns mean dissimilarities and
 	counts for classes. Expected delta is now the mean of original