[Vegan-commits] r945 - in pkg/vegan: inst man

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

Author: jarioksa
Date: 2009-08-24 21:20:58 +0200 (Mon, 24 Aug 2009)
New Revision: 945

Added:
   pkg/vegan/man/RsquareAdj.Rd
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/varpart.Rd
Log:
RsquareAdj documentation added

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-08-24 09:43:23 UTC (rev 944)
+++ pkg/vegan/inst/ChangeLog	2009-08-24 19:20:58 UTC (rev 945)
@@ -7,6 +7,8 @@
 	* mantel.correlog: updated to the version 1.4 of Pierre Legendre's
 	package. 
 
+	*  RsquareAdj documented.
+
 Version 1.16-24 (opened August 17, 2009)
 
 	* ordiellipse & ordihull: gained new argument 'label' to put the

Added: pkg/vegan/man/RsquareAdj.Rd
===================================================================
--- pkg/vegan/man/RsquareAdj.Rd	                        (rev 0)
+++ pkg/vegan/man/RsquareAdj.Rd	2009-08-24 19:20:58 UTC (rev 945)
@@ -0,0 +1,67 @@
+\name{RsquareAdj}
+\alias{RsquareAdj}
+\alias{RsquareAdj.default}
+\alias{RsquareAdj.rda}
+\alias{RsquareAdj.cca}
+\alias{RsquareAdj.lm}
+\alias{RsquareAdj.glm}
+
+\Rdversion{1.1}
+\alias{RsquareAdj}
+
+\title{
+Adjusted R-square
+}
+\description{
+  The functions finds the adjusted R-square.
+}
+\usage{
+\method{RsquareAdj}{default}(x, n, m, ...)
+\method{RsquareAdj}{rda}(x, ...)
+}
+
+\arguments{
+
+  \item{x}{ Unadjusted R-squared or an object from which the terms for
+  evaluation or adjusted R-squared can be found.  }
+  
+  \item{n, m}{Number of observations and number of degree of freedom
+  in the fitted model}
+
+  \item{\dots}{ Other arguments (ignored).  } }
+
+\details{ The default method of the function finds the adjusted
+  R-squared from the unadjusted R-squared, number of observations, and
+  number of degree of freedom in the fitted model. The specific
+  methods can found this information from the fitted result
+  object. There are specific methods fro \code{\link{rda}},
+  \code{\link{cca}}, \code{\link{lm}} and \code{\link{glm}}. Adjusted,
+  or even unandjusted, R-squared may not be available in some cases,
+  and then the functions will return \code{NA}. There is no adjusted
+  R-squared in \code{\link{cca}}, neither in partial \code{\link{rda}}, and
+  R-squared values are available only for \code{\link{gaussian}}
+  models in \code{\link{glm}}. 
+}
+
+\value{ The functions return a list of items \code{r.squared} and
+\code{adj.r.squared}.  }
+
+\references{ 
+  Peres-Neto, P., P. Legendre, S. Dray and D. Borcard. 2006. Variation
+  partioning of species data matrices: estimation and comparison of
+  fractions. \emph{Ecology} 87: 2614-2625.  }
+
+\seealso{
+  \code{\link{varpart}} uses \code{RsquareAdj}.
+}
+\examples{
+data(mite)
+data(mite.env)
+## rda
+m <- rda(decostand(mite, "hell") ~  ., mite.env)
+RsquareAdj(m)
+## default method
+RsquareAdj(0.8, 20, 5)
+}
+\keyword{ univar }
+\keyword{ multivariate }

Modified: pkg/vegan/man/varpart.Rd
===================================================================
--- pkg/vegan/man/varpart.Rd	2009-08-24 09:43:23 UTC (rev 944)
+++ pkg/vegan/man/varpart.Rd	2009-08-24 19:20:58 UTC (rev 945)
@@ -9,14 +9,6 @@
 \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 }