[Analogue-commits] r328 - pkg/man

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

Author: gsimpson
Date: 2013-05-13 07:39:07 +0200 (Mon, 13 May 2013)
New Revision: 328

Added:
   pkg/man/sppResponse.prcurve.Rd
Log:
document sppResponse

Added: pkg/man/sppResponse.prcurve.Rd
===================================================================
--- pkg/man/sppResponse.prcurve.Rd	                        (rev 0)
+++ pkg/man/sppResponse.prcurve.Rd	2013-05-13 05:39:07 UTC (rev 328)
@@ -0,0 +1,62 @@
+\name{sppResponse}
+\alias{sppResponse}
+\alias{sppResponse.prcurve}
+
+\title{Species responses along gradients.}
+\description{The fitted responses of species along gradients are
+  estimated or extracted from appropriate objects.}
+\usage{
+sppResponse(x, ...)
+
+\method{sppResponse}{prcurve}(x, n = 100, ...)
+}
+\arguments{
+  \item{x}{an R object.}
+  \item{n}{numeric; the number of locations on the gradient to evaluate
+    the response curve.}
+  \item{\dots}{additional arguments passed to other methods.}
+}
+\details{
+  \code{sppResponse} estimates species responses along indicated
+  gradients.
+
+  There is currently no \code{"default"} method and the only specified
+  method supplied is for objects fitted by \code{\link{prcurve}}. This
+  method extracts the fitted responses of species along the principal
+  curve and is a useful diagnostic for identifying overly-complex
+  curves.
+}
+\value{
+  A list is returned with components \code{observed} and
+  \code{fitted.values} containing the observed and fitted values of the
+  species response and gradient respectively. Each is a list with two
+  components, \code{gradient} and \code{response}, containing the
+  gradient and response values.
+}
+\author{Gavin L. Simpson}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+  \code{\link{prcurve}} for one function that can be used with
+  \code{sppResponse}. A \code{\link{plot}} method is available; see
+  \code{plot.sppResponse} for details.
+}
+\examples{
+## Load the Abernethy Forest data set
+data(abernethy)
+
+## Remove the Depth and Age variables
+abernethy2 <- abernethy[, -(37:38)]
+
+## Fit the principal curve using varying complexity of smoothers
+## for each species
+aber.pc <- prcurve(abernethy2, method = "ca", trace = TRUE,
+                   vary = TRUE, penalty = 1.4)
+
+## Extract the fitted species response curves
+resp <- sppResponse(aber.pc)
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ methods }