[Analogue-commits] r322 - pkg/man

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

Author: gsimpson
Date: 2013-05-13 06:55:07 +0200 (Mon, 13 May 2013)
New Revision: 322

Added:
   pkg/man/scores.prcurve.Rd
Removed:
   pkg/man/scores.prcurve.Rd
Log:
fix typo in arguments

Deleted: pkg/man/scores.prcurve.Rd
===================================================================
--- pkg/man/scores.prcurve.Rd	2013-05-10 19:06:15 UTC (rev 321)
+++ pkg/man/scores.prcurve.Rd	2013-05-13 04:55:07 UTC (rev 322)
@@ -1,68 +0,0 @@
-\name{scores.prcurve}
-\alias{scores.prcurve}
-
-\title{\code{\link[vegan]{scores}} method for principal curve objects of
-  class \code{"prcurve"}.}
-\description{
-  A \code{\link[vegan]{scores}} method to extract the position on the
-  curve to which each observation projects (\code{display = "curve"}) or
-  the coordinates of the curve in the dimensions of the input data
-  (\code{display = "dimensions"}).
-}
-\usage{
-\method{scores}{prcurve}(x, display = c("curve", "dimensions"), ...)
-}
-
-\arguments{
-  \item{x}{an object of class \code{"prcurve"}, usually from a call to
-    \code{\link{prcurve}}}.
-  \item{display}{character; which type of scores to
-    extract. \code{display = "curve"} returns the position along the curve
-    onto which each observation projects; this can be used like a PCA axis
-    score. \code{display = "dimensions"} returns the coordinates of the
-    curve in the dimensions of the original data.}
-  \item{\dots}{Arguments passed to other methods. Not used.}
-}
-%\details{
-%%  ~~ If necessary, more details than the description above ~~
-%}
-\value{
-  If \code{display = "curve"} a 1-column matrix is returned with a row
-  for each observation in the input data. If \code{display =
-  "dimensions"}, a matrix of coordinates for the principal curve is
-  returned. The dimensions of this matrix relate to the dimensions of
-  the input data; if there were \eqn{n} samples (rows) and \eqn{m}
-  variables {columns} then the matrix returned by \code{scores.prcurve}
-  will have \eqn{n} rows and \eqn{m} columns.
-}
-\author{Gavin L. Simpson}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-  \code{\link{prcurve}} for fitting principal curves to data.
-}
-\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 position on the curve
-pos <- scores(aber.pc, display = "curve")
-head(pos)
-
-## Extract the coordinates of the curve
-coord <- scores(aber.pc, display = "dimensions")
-dim(coord)
-all.equal(dim(coord), dim(abernethy2))
-}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-\keyword{ methods }

Added: pkg/man/scores.prcurve.Rd
===================================================================
--- pkg/man/scores.prcurve.Rd	                        (rev 0)
+++ pkg/man/scores.prcurve.Rd	2013-05-13 04:55:07 UTC (rev 322)
@@ -0,0 +1,68 @@
+\name{scores.prcurve}
+\alias{scores.prcurve}
+
+\title{\code{\link[vegan]{scores}} method for principal curve objects of
+  class \code{"prcurve"}.}
+\description{
+  A \code{\link[vegan]{scores}} method to extract the position on the
+  curve to which each observation projects (\code{display = "curve"}) or
+  the coordinates of the curve in the dimensions of the input data
+  (\code{display = "dimensions"}).
+}
+\usage{
+\method{scores}{prcurve}(x, display = c("curve", "dimensions"), ...)
+}
+
+\arguments{
+  \item{x}{an object of class \code{"prcurve"}, usually from a call to
+    \code{\link{prcurve}}.}
+  \item{display}{character; which type of scores to
+    extract. \code{display = "curve"} returns the position along the curve
+    onto which each observation projects; this can be used like a PCA axis
+    score. \code{display = "dimensions"} returns the coordinates of the
+    curve in the dimensions of the original data.}
+  \item{\dots}{Arguments passed to other methods. Not used.}
+}
+%\details{
+%%  ~~ If necessary, more details than the description above ~~
+%}
+\value{
+  If \code{display = "curve"} a 1-column matrix is returned with a row
+  for each observation in the input data. If \code{display =
+  "dimensions"}, a matrix of coordinates for the principal curve is
+  returned. The dimensions of this matrix relate to the dimensions of
+  the input data; if there were \eqn{n} samples (rows) and \eqn{m}
+  variables {columns} then the matrix returned by \code{scores.prcurve}
+  will have \eqn{n} rows and \eqn{m} columns.
+}
+\author{Gavin L. Simpson}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+  \code{\link{prcurve}} for fitting principal curves to data.
+}
+\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 position on the curve
+pos <- scores(aber.pc, display = "curve")
+head(pos)
+
+## Extract the coordinates of the curve
+coord <- scores(aber.pc, display = "dimensions")
+dim(coord)
+all.equal(dim(coord), dim(abernethy2))
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ methods }