[Vegan-commits] r809 - in pkg/vegan: . R inst man

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

Author: jarioksa
Date: 2009-04-21 11:54:57 +0200 (Tue, 21 Apr 2009)
New Revision: 809

Modified:
   pkg/vegan/DESCRIPTION
   pkg/vegan/R/RsquareAdj.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/varpart.Rd
Log:
Made RsquareAdj generic, with methods for 'rda', 'cca' (NA), 'lm' and 'glm' objects (on P Legendre's request)

Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION	2009-04-15 12:36:02 UTC (rev 808)
+++ pkg/vegan/DESCRIPTION	2009-04-21 09:54:57 UTC (rev 809)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
 Version: 1.16-18
-Date: April 15, 2009
+Date: April 21, 2009
 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/vegan/R/RsquareAdj.R
===================================================================
--- pkg/vegan/R/RsquareAdj.R	2009-04-15 12:36:02 UTC (rev 808)
+++ pkg/vegan/R/RsquareAdj.R	2009-04-21 09:54:57 UTC (rev 809)
@@ -1,9 +1,51 @@
-"RsquareAdj" <-
-function(x, n, m, ...)
+`RsquareAdj` <-
+    function(x, ...)
 {
+    UseMethod("RsquareAdj")
+}
+
+
+`RsquareAdj.default` <-
+    function(x, n, m, ...)
+{
     if (m >= (n-1))
         NA
     else
         1 - (1-x)*(n-1)/(n-m-1)
 }
 
+## Use this with rda() results
+`RsquareAdj.rda` <-
+    function(x, ...)
+{
+    R2 <- x$CCA$tot.chi/x$tot.chi
+    m <- x$CCA$rank
+    n <- 1 + m + x$CA$rank + ifelse(is.null(x$pCCA), 0, x$pCCA$rank)
+    radj <- RsquareAdj(R2, n, m)
+    list(r.squared = R2, adj.r.squared = radj)
+}
+
+## cca result: no RsquareAdj
+RsquareAdj.cca <-
+    function(x, ...)
+{
+    NA
+}
+
+## Linear model: take the result from the summary
+RsquareAdj.lm <-
+  function(x, ...)
+{
+    summary(x)[c("r.squared", "adj.r.squared")]
+}
+
+## Generalized linear model: R2-adj only with Gaussian model
+RsquareAdj.glm <-
+    function(x, ...)
+{
+    if (family(x)$family == "gaussian")
+        summary.lm(x)[c("r.squared", "adj.r.squared")]
+    else
+        NA
+}
+

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-04-15 12:36:02 UTC (rev 808)
+++ pkg/vegan/inst/ChangeLog	2009-04-21 09:54:57 UTC (rev 809)
@@ -2,7 +2,13 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
-Version 1.16-18
+Version 1.16-18 (opened April 21, 2009)
+
+	* RsquareAdj: defined as generic function. The old RsquareAdj is
+	now the "default" method, and there are specific methods for
+	"rda", "cca" (= NA), "lm" and "glm" objects. Not yet documented,
+	but functions are listed as aliases in varpart.Rd. On Pierre
+	Legendre's request.
 	
 Version 1.16-17 (closed April 15, 2009)
 

Modified: pkg/vegan/man/varpart.Rd
===================================================================
--- pkg/vegan/man/varpart.Rd	2009-04-15 12:36:02 UTC (rev 808)
+++ pkg/vegan/man/varpart.Rd	2009-04-21 09:54:57 UTC (rev 809)
@@ -9,7 +9,14 @@
 \alias{plot.varpart234}
 \alias{plot.varpart}
 \alias{plot.varpart234}
+% The RsquareAdj's should probably be documented in another file
 \alias{RsquareAdj}
+\alias{RsquareAdj.default}
+\alias{RsquareAdj.rda}
+\alias{RsquareAdj.cca}
+\alias{RsquareAdj.lm}
+\alias{RsquareAdj.glm}
+% End RsquareAdj's (to be moved away from here)
 \alias{simpleRDA2}
 
 \title{Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices }