[Vegan-commits] r2399 - in branches/2.0: R inst

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

Author: jarioksa
Date: 2013-01-31 14:48:28 +0100 (Thu, 31 Jan 2013)
New Revision: 2399

Modified:
   branches/2.0/R/print.protest.R
   branches/2.0/R/procrustes.R
   branches/2.0/inst/ChangeLog
Log:
merge 2385,7: protest and procrustes tweaks

Modified: branches/2.0/R/print.protest.R
===================================================================
--- branches/2.0/R/print.protest.R	2013-01-31 08:19:45 UTC (rev 2398)
+++ branches/2.0/R/print.protest.R	2013-01-31 13:48:28 UTC (rev 2399)
@@ -3,7 +3,9 @@
 {
   cat("\nCall:\n")
   cat(deparse(x$call), "\n\n")
-  cat("Correlation in a symmetric Procrustes rotation:  ")
+  cat("Procrustes Sum of Squares (m12 squared):        ")
+  cat(formatC(x$ss, digits=digits), "\n")
+  cat("Correlation in a symmetric Procrustes rotation: ")
   cat(formatC(x$t0, digits = digits), "\n")
   cat("Significance:  ")
   cat(format.pval(x$signif),"\n")

Modified: branches/2.0/R/procrustes.R
===================================================================
--- branches/2.0/R/procrustes.R	2013-01-31 08:19:45 UTC (rev 2398)
+++ branches/2.0/R/procrustes.R	2013-01-31 13:48:28 UTC (rev 2399)
@@ -11,7 +11,7 @@
         addcols <- ncol(Y) - ncol(X)
         for (i in 1:addcols) X <- cbind(X, 0)
     }
-    ctrace <- function(MAT) sum(diag(crossprod(MAT)))
+    ctrace <- function(MAT) sum(MAT^2)
     c <- 1
     if (symmetric) {
         X <- scale(X, scale = FALSE)

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-01-31 08:19:45 UTC (rev 2398)
+++ branches/2.0/inst/ChangeLog	2013-01-31 13:48:28 UTC (rev 2399)
@@ -8,6 +8,7 @@
 	data.frame. Not merged: checking length of statistic when setting
 	its name.
 	* merge 2932,3: matching names in treedive() and treedist().
+	* merge 2385, 7: protest print, faster sum of squares in procrustes. 
 	* merge 2384: new FAQ entries.
 	* merge 2383: remove alias to print.wcmdscale.
 	* merge 2374,2376,2378,2382: orditorp gains argument select