[Vegan-commits] r1355 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-11-09 10:23:48 +0100 (Tue, 09 Nov 2010)
New Revision: 1355

Modified:
   pkg/vegan/R/procrustes.R
   pkg/vegan/inst/ChangeLog
Log:
Procrustes translation needs scale: fix by Christian Dudel

Modified: pkg/vegan/R/procrustes.R
===================================================================
--- pkg/vegan/R/procrustes.R	2010-11-09 08:44:12 UTC (rev 1354)
+++ pkg/vegan/R/procrustes.R	2010-11-09 09:23:48 UTC (rev 1355)
@@ -29,10 +29,13 @@
         c <- sum(sol$d)/ctrace(Y)
     }
     Yrot <- c * Y %*% A
-    b <- xmean - t(A %*% ymean)
+    ## Translation (b) needs scale (c) although Mardia et al. do not
+    ## have this. Reported by Christian Dudel.
+    b <- xmean - c * ymean %*% A
     R2 <- ctrace(X) + c * c * ctrace(Y) - 2 * c * sum(sol$d)
     reslt <- list(Yrot = Yrot, X = X, ss = R2, rotation = A, 
-                  translation = b, scale = c, symmetric = symmetric, call = match.call())
+                  translation = b, scale = c, symmetric = symmetric,
+                  call = match.call())
     reslt$svd <- sol
     class(reslt) <- "procrustes"
     return(reslt)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-11-09 08:44:12 UTC (rev 1354)
+++ pkg/vegan/inst/ChangeLog	2010-11-09 09:23:48 UTC (rev 1355)
@@ -4,6 +4,10 @@
 
 Version 1.18-15 (opened November 1, 2010)
 
+	* procrustes: 'translation' needs to take into account 'scale',
+	although Mardia et al. omit it. Reported, analysed and fix
+	suggested by Christian Dudel (Bochum). 
+
 	* fitspecaccum: uses now new SS-models for species-area
 	relationship and several of standard SS-models for
 	nls(). Placeholders for documentation added. Has a plot()