[Vegan-commits] r492 - in pkg: . R inst man

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

Author: jarioksa
Date: 2008-09-05 14:14:54 +0200 (Fri, 05 Sep 2008)
New Revision: 492

Modified:
   pkg/DESCRIPTION
   pkg/R/permutest.cca.R
   pkg/inst/ChangeLog
   pkg/man/anova.cca.Rd
Log:
permutest.cca: default model 'reduced' (was 'direct')

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-09-01 14:45:07 UTC (rev 491)
+++ pkg/DESCRIPTION	2008-09-05 12:14:54 UTC (rev 492)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
-Version: 1.14-10
-Date: August 21, 2008
+Version: 1.14-11
+Date: September 5, 2008
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: pkg/R/permutest.cca.R
===================================================================
--- pkg/R/permutest.cca.R	2008-09-01 14:45:07 UTC (rev 491)
+++ pkg/R/permutest.cca.R	2008-09-05 12:14:54 UTC (rev 492)
@@ -5,7 +5,7 @@
     stop("No default permutation test defined")
 
 `permutest.cca` <-
-    function (x, permutations = 100, model = c("direct", "reduced", 
+    function (x, permutations = 100, model = c("reduced", "direct", 
                                      "full"), first = FALSE, strata, ...) 
 {
     model <- match.arg(model)

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2008-09-01 14:45:07 UTC (rev 491)
+++ pkg/inst/ChangeLog	2008-09-05 12:14:54 UTC (rev 492)
@@ -3,8 +3,18 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.14-10 (opened August 21, 2008)
+Version 1.14-11 (opened September 5, 2008)
 
+	* anova.cca/permutest.cca: default permutation model changed from
+	"direct" to "reduced" after Pierre Legendre's simulation test
+	demonstrated slightly better Type I error for "reduced" models in
+	by = "axis" and other partial models. This is also consistent with
+	CANOCO (but permutation of CCA residuals differs from CANOCO). For
+	compatibility with old versions of vegan, you must set model =
+	"direct" explicitly.
+	
+Version 1.14-10 (closed September 5, 2008)
+
 	* treedive: tries to match 'comm' and 'tree' names if forced (by
 	an arg), or when sizes do not match. Output vector has names. Docs
 	discuss estimating signifcance using oecosimu().

Modified: pkg/man/anova.cca.Rd
===================================================================
--- pkg/man/anova.cca.Rd	2008-09-01 14:45:07 UTC (rev 491)
+++ pkg/man/anova.cca.Rd	2008-09-05 12:14:54 UTC (rev 492)
@@ -23,7 +23,7 @@
 permutest(x, ...)
 
 \method{permutest}{cca}(x, permutations = 100,
-          model = c("direct", "reduced", "full"),
+          model = c("reduced", "direct", "full"),
           first = FALSE, strata, ...)
 }
 
@@ -59,7 +59,7 @@
   \code{anova.cca} passes all parameters to \code{permutest.cca}.
 
   In \code{anova.cca} the number of permutations is controlled by
-  targeted ``critical'' \eqn{P} value (\code{alpha}) and accepted Type
+  targeted \dQuote{critical} \eqn{P} value (\code{alpha}) and accepted Type
   II or rejection error (\code{beta}).  If the results of permutations
   differ from the targeted \code{alpha} at risk level given by
   \code{beta}, the permutations are
@@ -73,19 +73,20 @@
   by \code{step}.  
   
   The function \code{permutest.cca} implements a permutation test for
-  the ``significance'' of constraints in \code{\link{cca}},
+  the \dQuote{significance} of constraints in \code{\link{cca}},
   \code{\link{rda}} or \code{\link{capscale}}.  Community data are
   permuted with choice \code{model = "direct"}, residuals after
-  partial CCA/RDA/CAP with choice \code{model = "reduced"},
+  partial CCA/RDA/CAP with choice \code{model = "reduced"} (default),
   and residuals after CCA/RDA/CAP under choice \code{model = "full"}.
   If there is no partial CCA/RDA/CAP stage, \code{model = "reduced"}
-  simply permutes the data. The test statistic is ``pseudo-\eqn{F}'',
+  simply permutes the data and is equivalent to \code{model = "direct"}. 
+  The test statistic is ``pseudo-\eqn{F}'',
   which is the ratio of constrained and unconstrained total Inertia
   (Chi-squares, variances or something similar), each divided by their
-  respective ranks.  If there are no conditions ("partial" terms), the
+  respective ranks.  If there are no conditions (\dQuote{partial} terms), the
   sum of all eigenvalues remains constant, so that pseudo-\eqn{F} and
   eigenvalues would give equal results.  In partial CCA/RDA/CAP, the
-  effect of conditioning variables (``covariables'') is removed before
+  effect of conditioning variables (\dQuote{covariables} is removed before
   permutation, and these residuals are added to the non-permuted fitted
   values of partial CCA (fitted values of \code{X ~ Z}).  Consequently,
   the total Chi-square is not fixed, and test based on pseudo-\eqn{F}
@@ -122,6 +123,12 @@
   function \code{anova.cca} calls \code{permutest.cca}, fills an
   \code{\link{anova}} table and uses \code{\link{print.anova}} for printing.
 }
+\note{
+  The default permutation \code{model} changed from \code{"direct"} to
+  \code{"reduced"} in \pkg{vegan} version 1.14-11 (release version
+  1.15-0), and you must explicitly set \code{model = "direct"} for
+  compatibility with the old version.
+}
 \references{
   Legendre, P. and Legendre, L. (1998). \emph{Numerical Ecology}. 2nd English
   ed. Elsevier.