[Vegan-commits] r2257 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2012-08-23 08:21:08 +0200 (Thu, 23 Aug 2012)
New Revision: 2257

Modified:
   pkg/vegan/R/protest.R
   pkg/vegan/inst/ChangeLog
Log:
do not return observed statistic as one of permuted values

Modified: pkg/vegan/R/protest.R
===================================================================
--- pkg/vegan/R/protest.R	2012-08-22 06:39:27 UTC (rev 2256)
+++ pkg/vegan/R/protest.R	2012-08-23 06:21:08 UTC (rev 2257)
@@ -23,8 +23,7 @@
                    function(i, ...) procrustes(X, Y[permat[i,],],
                                                symmetric = TRUE)$ss)
     perm <- sqrt(1 - perm)
-    perm <- c(sol$t0, perm)
-    Pval <- sum(perm >= sol$t0)/(permutations + 1)
+    Pval <- (sum(perm >= sol$t0) + 1)/(permutations + 1)
     if (!missing(strata)) {
         strata <- deparse(substitute(strata))
         s.val <- strata

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-08-22 06:39:27 UTC (rev 2256)
+++ pkg/vegan/inst/ChangeLog	2012-08-23 06:21:08 UTC (rev 2257)
@@ -22,6 +22,9 @@
 	Functions adipart, hiersimu and multipart were made
 	oecosimu-compliant earlier and simultaneously they also gained the
 	density and densityplot methods.
+
+	* protest: do not return the observed statistic as one of the
+	permuted values but separately.
 	
 Version 2.1-18 (closed August 20, 2012)