[Vegan-commits] r2484 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2013-04-07 08:00:57 +0200 (Sun, 07 Apr 2013)
New Revision: 2484

Modified:
   pkg/vegan/R/betadisper.R
   pkg/vegan/inst/ChangeLog
Log:
betadisper(..., type = 'centroid') failed when there was only one group

Modified: pkg/vegan/R/betadisper.R
===================================================================
--- pkg/vegan/R/betadisper.R	2013-03-19 14:22:26 UTC (rev 2483)
+++ pkg/vegan/R/betadisper.R	2013-04-07 06:00:57 UTC (rev 2484)
@@ -92,11 +92,13 @@
     ## Uses in-line Resids function as we want LAD residuals for
     ## median method, and LSQ residuals for centroid method
     dist.pos <- Resids(vectors[, pos, drop=FALSE],
-                       centroids[group, pos, drop=FALSE])
+                       if (is.vector(centroids)) centroids[pos]
+                       else centroids[group, pos, drop=FALSE])
     dist.neg <- 0
     if(any(!pos))
         dist.neg <- Resids(vectors[, !pos, drop=FALSE],
-                           centroids[group, !pos, drop=FALSE])
+                           if (is.vector(centroids)) centroids[!pos]
+                           else centroids[group, !pos, drop=FALSE])
 
     ## zij are the distances of each point to its group centroid
     zij <- sqrt(abs(dist.pos - dist.neg))

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-03-19 14:22:26 UTC (rev 2483)
+++ pkg/vegan/inst/ChangeLog	2013-04-07 06:00:57 UTC (rev 2484)
@@ -4,6 +4,10 @@
 
 Version 2.1-28 (opened March 17, 2013)
 
+	* betadisper: failed with type = "centroid" when there was only
+	one group (i.e., in estimating the overall beta diversity in the
+	data). Reported by Pierre Legendre.
+
 	* rda: eigenvalues are now regarded as zero if they are very small
 	compared to the first eigenvalue. Earlier we used fixed limit of
 	1e-4, but now the limit is first eigenvalues * 1e-5. Similar