[Vegan-commits] r1039 - in pkg/vegan: inst man

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

Author: jarioksa
Date: 2009-10-08 17:09:52 +0200 (Thu, 08 Oct 2009)
New Revision: 1039

Added:
   pkg/vegan/man/model.matrix.cca.Rd
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/cca.Rd
Log:
documentation of model.frame.cca & model.matrix.cca

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-10-07 17:55:56 UTC (rev 1038)
+++ pkg/vegan/inst/ChangeLog	2009-10-08 15:09:52 UTC (rev 1039)
@@ -7,8 +7,7 @@
 	* model.frame.cca, model.matrix.cca: new support functions to
 	reconstitute the model frame and model matrix (or  a list of
 	condition and constrain model matrices) from a cca/rda/capscale
-	result object. Not yet documentd (don't know where?), but alias is
-	in cca.Rd.
+	result object. Documented separately.
 
 	* constrained ordination (cca, rda, capscale) did not analyse
 	constrained component in model like cca(varespec ~ Al:P +

Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd	2009-10-07 17:55:56 UTC (rev 1038)
+++ pkg/vegan/man/cca.Rd	2009-10-08 15:09:52 UTC (rev 1039)
@@ -6,8 +6,6 @@
 \alias{rda}
 \alias{rda.default}
 \alias{rda.formula}
-\alias{model.frame.cca} % <- Move to a better help page!!
-\alias{model.matrix.cca} % <- Move to a better help page!
 \concept{ordination}
 
 \title{ [Partial] [Constrained] Correspondence Analysis and Redundancy

Added: pkg/vegan/man/model.matrix.cca.Rd
===================================================================
--- pkg/vegan/man/model.matrix.cca.Rd	                        (rev 0)
+++ pkg/vegan/man/model.matrix.cca.Rd	2009-10-08 15:09:52 UTC (rev 1039)
@@ -0,0 +1,57 @@
+\name{model.matrix.cca}
+\Rdversion{1.1}
+\alias{model.matrix.cca}
+\alias{model.frame.cca}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+ Reconstruct Model Frame and Model Matrices of Constrained Ordination
+}
+\description{
+  Function \code{model.frame.cca} reconstructs a \code{\link{data.frame}}
+  with the variables used in the constrained ordination method 
+  (\code{\link{cca}}, \code{\link{rda}} or \code{\link{capscale}}. 
+  Function \code{model.matrix.cca} creates a list of design matrices used 
+  in constrained ordination. The items of the list are called 
+  \code{Conditions} and \code{Constraints}. If either partial 
+  (\code{Conditions}) or constrained component was missing, 
+  a single matrix is returned. 
+}
+\usage{
+model.matrix.cca(formula, ...)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{formula, object}{
+  A constrained ordination result object from which the needed
+  information is extracted.
+}
+  \item{\dots}{
+  Other arguments passed to the default method of the function.
+}
+}
+\details{
+  The constrained ordination method objects do not save data on model 
+  frame or design matrix, and the functions must reconstruct the
+  information in the session. This will fail if the data sets and variables
+  of the original model are unavailable.
+}
+\value{
+  Returns a data frame (\code{model.frame}) or an unnnamed matrix or a list 
+  of two matrices called \code{Constraints} and \code{Conditions} 
+  (\code{model.matrix}). 
+}
+\author{
+ Jari Oksanen
+
+\seealso{
+ \code{\link{model.frame}}, \code{\link{model.matrix}}.
+}
+\examples{
+data(dune)
+data(dune.env)
+mod <- cca(dune ~  poly(A1, 2) + Management + Use, dune.env)
+model.frame(mod)
+model.matrix(mod)
+}
+\keyword{ models }
+\keyword{ multivariate }