[Vegan-commits] r2406 - in branches/2.0: R inst

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

Author: jarioksa
Date: 2013-02-04 18:45:14 +0100 (Mon, 04 Feb 2013)
New Revision: 2406

Modified:
   branches/2.0/R/protest.R
   branches/2.0/inst/ChangeLog
Log:
merge r2388: faster protest, partly hand crafted

Modified: branches/2.0/R/protest.R
===================================================================
--- branches/2.0/R/protest.R	2013-02-04 17:01:55 UTC (rev 2405)
+++ branches/2.0/R/protest.R	2013-02-04 17:45:14 UTC (rev 2406)
@@ -3,14 +3,26 @@
 {
     X <- scores(X, display = scores, ...)
     Y <- scores(Y, display = scores, ...)
-    sol <- procrustes(X, Y, symmetric = TRUE)
+    ## Centre and normalize X & Y here so that the permutations will
+    ## be faster
+    X <- scale(X, scale = FALSE)
+    Y <- scale(Y, scale = FALSE)
+    X <- X/sqrt(sum(X^2))
+    Y <- Y/sqrt(sum(Y^2))
+    ## Transformed X and Y will yield symmetric procrustes() and we
+    ## need not specify that in the call (but we set it symmetric
+    ## after the call).
+    sol <- procrustes(X, Y, symmetric = FALSE)
+    sol$symmetric <- TRUE
     sol$t0 <- sqrt(1 - sol$ss)
     N <- nrow(X)
     perm <- rep(0, permutations)
     for (i in 1:permutations) {
         take <- permuted.index(N, strata)
-        tmp <- procrustes(X, Y[take, ], symmetric = TRUE)$ss
-        perm[i] <- sqrt(1 - tmp)
+        ## avoid overhead of procrustes() and only evaluate the
+        ## statistic by svd (hand crafted from r2388 of the devel
+        ## branch).
+        perm[i] <- sum(svd(crossprod(X, Y[take,]), nv = 0, nu = 0)$d)
     }
     Pval <- (sum(perm >= sol$t0) + 1)/(permutations + 1)
     if (!missing(strata)) {

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-02-04 17:01:55 UTC (rev 2405)
+++ branches/2.0/inst/ChangeLog	2013-02-04 17:45:14 UTC (rev 2406)
@@ -4,10 +4,15 @@
 
 Version 2.0-6 (opened October 8, 2012)
 
+	* merge 2404: refer Legendre & Legendre for the vegan rda
+	algorithm. 
 	* merge 2934 (partial, mc): oecosimu handles nestedfun() returning
 	data.frame. Not merged: checking length of statistic when setting
 	its name.
 	* merge 2932,3: matching names in treedive() and treedist().
+	* merge 2388 (partial): faster protest, the part of evaluating the
+	test statistic hand crafted, because parallelizations caused
+	conflicts here.
 	* merge 2385, 7: protest print, faster sum of squares in procrustes. 
 	* merge 2384: new FAQ entries.
 	* merge 2383: remove alias to print.wcmdscale.