[Vegan-commits] r1380 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-11-23 16:58:39 +0100 (Tue, 23 Nov 2010)
New Revision: 1380

Modified:
   pkg/vegan/R/mantel.correlog.R
   pkg/vegan/inst/ChangeLog
Log:
remove a fix that tried to fix a fixed thing

Modified: pkg/vegan/R/mantel.correlog.R
===================================================================
--- pkg/vegan/R/mantel.correlog.R	2010-11-23 15:54:15 UTC (rev 1379)
+++ pkg/vegan/R/mantel.correlog.R	2010-11-23 15:58:39 UTC (rev 1380)
@@ -95,10 +95,12 @@
                 temp <- mantel(mat.D2, D.eco, method=r.type, permutations=nperm)
                 mantel.r <- c(mantel.r, -temp$statistic)
                 temp.p <- temp$signif
-                if(temp$statistic >= 0) {
-                    temp.p <- ((temp.p*nperm)+1)/(nperm+1)
-                } else {
-                    temp.p <- (((1-temp.p)*nperm)+1)/(nperm+1)
+                
+                ## The mantel() function produces a one-tailed p-value
+                ## (H1: r>0) Here, compute a one-tailed p-value in
+                ## direction of the sign
+                if(temp$statistic < 0) {
+                    temp.p <- ((1-temp.p)*(nperm+1))/(nperm+1)
                 }
                 mantel.p <- c(mantel.p, temp.p)
             } else {

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-11-23 15:54:15 UTC (rev 1379)
+++ pkg/vegan/inst/ChangeLog	2010-11-23 15:58:39 UTC (rev 1380)
@@ -8,6 +8,11 @@
 	vegan. Mainly clean up and checking of functions intended for the
 	release. 
 
+	* mantel.correlog: vegan mantel() was used standard order
+	statistics or (hits+1)/(nperm+1) since May 2009, but
+	mantel.correlog() did not notice the change and still tried to
+	correct the mantel() result.
+
 	* as.mlm.cca/rda and intersector: should get the pivoting of names
 	in qr.X() correct both in the current buggy R and hopefully fixed
 	next version 2.12.1.