[Vegan-commits] r848 - in branches/1.15: R inst man

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

Author: jarioksa
Date: 2009-06-01 11:23:02 +0200 (Mon, 01 Jun 2009)
New Revision: 848

Modified:
   branches/1.15/R/protest.R
   branches/1.15/inst/ChangeLog
   branches/1.15/man/procrustes.Rd
Log:
forgot to merge Gav's r834 that started all this putting obs to permutations fixes (protest)

Modified: branches/1.15/R/protest.R
===================================================================
--- branches/1.15/R/protest.R	2009-06-01 08:36:37 UTC (rev 847)
+++ branches/1.15/R/protest.R	2009-06-01 09:23:02 UTC (rev 848)
@@ -1,5 +1,5 @@
 "protest" <-
-    function (X, Y, scores = "sites", permutations = 1000, strata, ...) 
+    function (X, Y, scores = "sites", permutations = 999, strata, ...)
 {
     X <- scores(X, display = scores, ...)
     Y <- scores(Y, display = scores, ...)
@@ -12,6 +12,8 @@
         tmp <- procrustes(X, Y[take, ], symmetric = TRUE)$ss
         perm[i] <- sqrt(1 - tmp)
     }
+    perm <- c(sol$t0, perm)
+    permutations <- permutations + 1
     Pval <- sum(perm >= sol$t0)/permutations
     if (!missing(strata)) {
         strata <- deparse(substitute(strata))

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-06-01 08:36:37 UTC (rev 847)
+++ branches/1.15/inst/ChangeLog	2009-06-01 09:23:02 UTC (rev 848)
@@ -5,11 +5,11 @@
 
 Version 1.15-3 (opened 28 May, 2009)
 
-	* merged r837:r842 and r846 that put the observed test statistic
-	among permutations like should be done with order statistics.
-	Concerns functions anosim, mantel, mantel.partial, mrpp, protest,
-	factorfit, vectorfit. General cleanup also concerns adonis and
-	permutest.cca. 
+	* merged r834, r837:r842 and r846 that put the observed test
+	statistic among permutations like should be done with order
+	statistics.  Concerns functions anosim, mantel, mantel.partial,
+	mrpp, protest, factorfit, vectorfit. General cleanup also concerns
+	adonis and permutest.cca.
 
 	* merged r832: wrong reference in metaMDS.Rd.
 	

Modified: branches/1.15/man/procrustes.Rd
===================================================================
--- branches/1.15/man/procrustes.Rd	2009-06-01 08:36:37 UTC (rev 847)
+++ branches/1.15/man/procrustes.Rd	2009-06-01 09:23:02 UTC (rev 848)
@@ -28,7 +28,7 @@
 \method{lines}{procrustes}(x, type = c("segments", "arrows"), choices = c(1, 2), ...)  
 \method{residuals}{procrustes}(object, ...)
 \method{fitted}{procrustes}(object, truemean = TRUE, ...)
-protest(X, Y, scores = "sites", permutations = 1000, strata, ...)
+protest(X, Y, scores = "sites", permutations = 999, strata, ...)
 }
 
 \arguments{