[Vegan-commits] r430 - in pkg: R inst

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

Author: jarioksa
Date: 2008-06-16 11:55:50 +0200 (Mon, 16 Jun 2008)
New Revision: 430

Modified:
   pkg/R/permutest.cca.R
   pkg/inst/ChangeLog
Log:
permutest.cca estimates now residual df from the number of rwos of data instead of the rank

Modified: pkg/R/permutest.cca.R
===================================================================
--- pkg/R/permutest.cca.R	2008-06-16 09:24:18 UTC (rev 429)
+++ pkg/R/permutest.cca.R	2008-06-16 09:55:50 UTC (rev 430)
@@ -22,7 +22,7 @@
     }
     Chi.xz <- x$CA$tot.chi
     names(Chi.xz) <- "Residual"
-    r <- x$CA$rank
+    r <- nrow(x$CA$Xbar) - x$CCA$QR$rank - 1
     if (model == "full") 
         Chi.tot <- Chi.xz
     else Chi.tot <- Chi.z + Chi.xz
@@ -96,4 +96,3 @@
     class(sol) <- "permutest.cca"
     sol
 }
-

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-06-16 09:24:18 UTC (rev 429)
+++ pkg/inst/ChangeLog	2008-06-16 09:55:50 UTC (rev 430)
@@ -18,6 +18,16 @@
 	* summary.cca: prints 'capscale' like 'rda' (used to have some
 	'cca' style output, like calling site scores "weighted averages"
 	instead of "weigthed sums").
+
+	* permutest.cca: estimates now residual df as number-of-rows -
+	rank-of-constraints-and-conditions - 1 so that df and pseudo-F are
+	equal to those reported by lm() for single response variables in
+	rda. anova(..., by = "ax") needs rethinking though: it only had
+	one df.  Because the test was based on permutation and order
+	statistics the change of df does not change the significances:
+	the observed pseudo-F and permuted pseudo-F's are influenced
+	similarly by the change of df, and order statistic does not
+	change. 
 	
 Version 1.14-4 (closed June 12, 2008)