[Archetypes-commits] r57 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 2 22:28:31 CEST 2012
Author: manuel
Date: 2012-05-02 22:28:30 +0200 (Wed, 02 May 2012)
New Revision: 57
Added:
pkg/man/predict.Rd
Modified:
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/archetypes-class.R
pkg/R/archetypes-kit.R
pkg/man/archetypes-generics.Rd
pkg/man/as.archetypes.Rd
Log:
predict.
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-04-26 13:33:11 UTC (rev 56)
+++ pkg/DESCRIPTION 2012-05-02 20:28:30 UTC (rev 57)
@@ -1,42 +1,42 @@
-Package: archetypes
-Type: Package
-Title: Archetypal Analysis
-Version: 2.1-0
-Date: 2011-10-25
-Depends:
- methods,
- stats,
- modeltools,
- nnls (>= 1.1)
-Suggests:
- MASS,
- vcd,
- mlbench,
- ggplot2
-Author: Manuel J. A. Eugster
- <manuel.eugster at stat.uni-muenchen.de>
-Maintainer: Manuel J. A. Eugster
- <manuel.eugster at stat.uni-muenchen.de>
-Description: The main function archetypes implements a
- framework for archetypal analysis supporting arbitary
- problem solving mechanisms for the different conceputal
- parts of the algorithm.
-License: GPL (>= 2)
-Revision: 44
-Collate:
- 'archetypes-barplot.R'
- 'generics.R'
- 'archetypes-class.R'
- 'archetypes-kit-blocks.R'
- 'archetypes-kit.R'
- 'archetypes-movie.R'
- 'archetypes-panorama.R'
- 'pcplot.R'
- 'archetypes-pcplot.R'
- 'archetypes-robust.R'
- 'archetypes-screeplot.R'
- 'archetypes-step.R'
- 'archetypes-weighted.R'
- 'archetypes-xyplot.R'
- 'memento.R'
- 'skeletonplot.R'
+Package: archetypes
+Type: Package
+Title: Archetypal Analysis
+Version: 2.1-0
+Date: 2011-10-25
+Depends:
+ methods,
+ stats,
+ modeltools,
+ nnls (>= 1.1)
+Suggests:
+ MASS,
+ vcd,
+ mlbench,
+ ggplot2
+Author: Manuel J. A. Eugster
+ <manuel.eugster at stat.uni-muenchen.de>
+Maintainer: Manuel J. A. Eugster
+ <manuel.eugster at stat.uni-muenchen.de>
+Description: The main function archetypes implements a
+ framework for archetypal analysis supporting arbitary
+ problem solving mechanisms for the different conceputal
+ parts of the algorithm.
+License: GPL (>= 2)
+Revision: 44
+Collate:
+ 'archetypes-barplot.R'
+ 'generics.R'
+ 'archetypes-class.R'
+ 'archetypes-kit-blocks.R'
+ 'archetypes-kit.R'
+ 'archetypes-movie.R'
+ 'archetypes-panorama.R'
+ 'pcplot.R'
+ 'archetypes-pcplot.R'
+ 'archetypes-robust.R'
+ 'archetypes-screeplot.R'
+ 'archetypes-step.R'
+ 'archetypes-weighted.R'
+ 'archetypes-xyplot.R'
+ 'memento.R'
+ 'skeletonplot.R'
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2012-04-26 13:33:11 UTC (rev 56)
+++ pkg/NAMESPACE 2012-05-02 20:28:30 UTC (rev 57)
@@ -36,6 +36,7 @@
S3method(panorama,archetypes)
S3method(pcplot,archetypes)
S3method(pcplot,default)
+S3method(predict,archetypes)
S3method(print,archetypes)
S3method(print,repArchetypes)
S3method(print,stepArchetypes)
Modified: pkg/R/archetypes-class.R
===================================================================
--- pkg/R/archetypes-class.R 2012-04-26 13:33:11 UTC (rev 56)
+++ pkg/R/archetypes-class.R 2012-05-02 20:28:30 UTC (rev 57)
@@ -23,6 +23,7 @@
#' @param residuals The residuals.
#' @param weights The data weights.
#' @param reweights The data reweights.
+#' @param scaling The scaling parameters of the data.
#'
#' @return A list with an element for each parameter and class attribute
#' \code{archetypes}.
@@ -33,7 +34,7 @@
as.archetypes <- function(object, k, alphas, rss, iters = NULL, call = NULL,
history = NULL, kappas = NULL, betas = NULL, zas = NULL,
family = NULL, familyArgs = NULL, residuals = NULL,
- weights = NULL, reweights = NULL) {
+ weights = NULL, reweights = NULL, scaling = NULL) {
return(structure(list(archetypes = object,
k = k,
@@ -49,7 +50,8 @@
familyArgs = familyArgs,
residuals = residuals,
weights = weights,
- reweights = reweights),
+ reweights = reweights,
+ scaling = scaling),
class = c(family$class, 'archetypes')))
}
@@ -212,20 +214,35 @@
-### Not implemented yet: #############################################
+#' Predict method for archetypal analysis
+#'
+#' @param object An \code{archetypes} object.
+#' @param newdata A data frame with data for which to
+#' predict the alpha coefficients.
+#' @param ... Ignored.
+#' @return The predict alpha coefficients.
+#' @rdname predict
+#'
+#' @method predict archetypes
+#' @S3method predict archetypes
+predict.archetypes <- function(object, newdata, ...) {
+ stopifnot(object$family$which == "original")
+
+ scale <- object$scaling
-predict.archetypes <- function(object, newdata = NULL,
- type = c('alphas', 'data'), ...) {
- type <- match.arg(type)
+ ## HACK: use blocks!
+ x <- t(newdata)
+ x <- x - scale$mean
+ x <- x / scale$sd
+ x <- object$family$dummyfn(x, ...)
- if ( is.null(newdata) )
- return(switch(type,
- alphas = coef(object, type = 'alphas'),
- data = fitted(object)))
+ zs <- t(parameters(object))
+ zs <- zs - scale$mean
+ zs <- zs / scale$sd
+ zs <- rbind(zs, 200)
- stop('Not implemented yet.')
+ alphas <- matrix(NA, ncol = ncol(x), nrow = ncol(coef(object)))
+ alphas <- object$family$alphasfn(alphas, zs, x)
- ### Something like the following ...
- #if ( type == 'alphas' )
- # object$family$alphasfn(NULL, t(object$archetypes), t(newdata))
+ t(alphas)
}
Modified: pkg/R/archetypes-kit.R
===================================================================
--- pkg/R/archetypes-kit.R 2012-04-26 13:33:11 UTC (rev 56)
+++ pkg/R/archetypes-kit.R 2012-05-02 20:28:30 UTC (rev 57)
@@ -177,7 +177,8 @@
call = mycall, history = memento, kappas = kappas,
betas = t(betas), family = family,
familyArgs = famargs, residuals = t(resid),
- weights = weights, reweights = reweights))
+ weights = weights, reweights = reweights,
+ scaling = attr(x1, ".Meta")))
}
Modified: pkg/man/archetypes-generics.Rd
===================================================================
--- pkg/man/archetypes-generics.Rd 2012-04-26 13:33:11 UTC (rev 56)
+++ pkg/man/archetypes-generics.Rd 2012-05-02 20:28:30 UTC (rev 57)
@@ -1,37 +1,37 @@
-\name{rss}
-\alias{bestModel}
-\alias{nparameters}
-\alias{panorama}
-\alias{pcplot}
-\alias{rss}
-\title{Defined generics}
-\usage{
- rss(object, ...)
-
- nparameters(object, ...)
-
- bestModel(object, ...)
-
- panorama(object, ...)
-
- pcplot(x, ...)
-}
-\arguments{
- \item{object}{An object}
-
- \item{...}{Futher arguments}
-
- \item{x}{An object.}
-}
-\description{
- Generics defined by the archetypes package.
-
- Return number of parameters
-
- Return best model
-
- Panorama
-
- Parallel coordinates plot
-}
-
+\name{rss}
+\alias{bestModel}
+\alias{nparameters}
+\alias{panorama}
+\alias{pcplot}
+\alias{rss}
+\title{Defined generics}
+\usage{
+ rss(object, ...)
+
+ nparameters(object, ...)
+
+ bestModel(object, ...)
+
+ panorama(object, ...)
+
+ pcplot(x, ...)
+}
+\arguments{
+ \item{object}{An object}
+
+ \item{...}{Futher arguments}
+
+ \item{x}{An object.}
+}
+\description{
+ Generics defined by the archetypes package.
+
+ Return number of parameters
+
+ Return best model
+
+ Panorama
+
+ Parallel coordinates plot
+}
+
Property changes on: pkg/man/archetypes-generics.Rd
___________________________________________________________________
Added: svn:keywords
+ Date Revision Author URL Id
Added: svn:eol-style
+ native
Modified: pkg/man/as.archetypes.Rd
===================================================================
--- pkg/man/as.archetypes.Rd 2012-04-26 13:33:11 UTC (rev 56)
+++ pkg/man/as.archetypes.Rd 2012-05-02 20:28:30 UTC (rev 57)
@@ -1,65 +1,67 @@
-\name{as.archetypes}
-\alias{as.archetypes}
-\title{Archetypes object constructor}
-\usage{
- as.archetypes(object, k, alphas, rss, iters = NULL,
- call = NULL, history = NULL, kappas = NULL,
- betas = NULL, zas = NULL, family = NULL,
- familyArgs = NULL, residuals = NULL, weights = NULL,
- reweights = NULL)
-}
-\arguments{
- \item{object}{The archetypes; a \eqn{p \times m} matrix,
- see \code{\link{parameters}}.}
-
- \item{k}{The number of archetypes;}
-
- \item{alphas}{The coefficients; a \eqn{n \times p}
- matrix, see \code{\link{coef}}.}
-
- \item{rss}{The residual sum of squares; see
- \code{\link{rss.archetypes}}.}
-
- \item{iters}{The number of iterations to the
- convergence.}
-
- \item{call}{The call of the \code{\link{archetypes}}
- function.}
-
- \item{history}{If \code{saveHistory} set then an
- environment with the archetypes object for each execution
- step;}
-
- \item{kappas}{The kappas for each system of linear
- equations.}
-
- \item{betas}{The data coefficients; a \eqn{p \times n}
- matrix.}
-
- \item{zas}{The temporary archetypes.}
-
- \item{family}{The archetypes family.}
-
- \item{familyArgs}{Additional arguments for family
- blocks.}
-
- \item{residuals}{The residuals.}
-
- \item{weights}{The data weights.}
-
- \item{reweights}{The data reweights.}
-}
-\value{
- A list with an element for each parameter and class
- attribute \code{archetypes}.
-}
-\description{
- Archetypes object constructor
-}
-\seealso{
- Other archetypes: \code{\link{archetypes}},
- \code{\link{archetypesFamily}},
- \code{\link{robustArchetypes}},
- \code{\link{weightedArchetypes}}
-}
-
+\name{as.archetypes}
+\alias{as.archetypes}
+\title{Archetypes object constructor}
+\usage{
+ as.archetypes(object, k, alphas, rss, iters = NULL,
+ call = NULL, history = NULL, kappas = NULL,
+ betas = NULL, zas = NULL, family = NULL,
+ familyArgs = NULL, residuals = NULL, weights = NULL,
+ reweights = NULL, scaling = NULL)
+}
+\arguments{
+ \item{object}{The archetypes; a \eqn{p \times m} matrix,
+ see \code{\link{parameters}}.}
+
+ \item{k}{The number of archetypes;}
+
+ \item{alphas}{The coefficients; a \eqn{n \times p}
+ matrix, see \code{\link{coef}}.}
+
+ \item{rss}{The residual sum of squares; see
+ \code{\link{rss.archetypes}}.}
+
+ \item{iters}{The number of iterations to the
+ convergence.}
+
+ \item{call}{The call of the \code{\link{archetypes}}
+ function.}
+
+ \item{history}{If \code{saveHistory} set then an
+ environment with the archetypes object for each execution
+ step;}
+
+ \item{kappas}{The kappas for each system of linear
+ equations.}
+
+ \item{betas}{The data coefficients; a \eqn{p \times n}
+ matrix.}
+
+ \item{zas}{The temporary archetypes.}
+
+ \item{family}{The archetypes family.}
+
+ \item{familyArgs}{Additional arguments for family
+ blocks.}
+
+ \item{residuals}{The residuals.}
+
+ \item{weights}{The data weights.}
+
+ \item{reweights}{The data reweights.}
+
+ \item{scaling}{The scaling parameters of the data.}
+}
+\value{
+ A list with an element for each parameter and class
+ attribute \code{archetypes}.
+}
+\description{
+ Archetypes object constructor
+}
+\seealso{
+ Other archetypes: \code{\link{archetypes}},
+ \code{\link{archetypesFamily}},
+ \code{\link{robustArchetypes}},
+ \code{\link{weightedArchetypes}}
+}
+
Added: pkg/man/predict.Rd
===================================================================
--- pkg/man/predict.Rd (rev 0)
+++ pkg/man/predict.Rd 2012-05-02 20:28:30 UTC (rev 57)
@@ -0,0 +1,21 @@
+\name{predict.archetypes}
+\alias{predict.archetypes}
+\title{Predict method for archetypal analysis}
+\usage{
+ \method{predict}{archetypes} (object, newdata, ...)
+}
+\arguments{
+ \item{object}{An \code{archetypes} object.}
+
+ \item{newdata}{A data frame with data for which to
+ predict the alpha coefficients.}
+
+ \item{...}{Ignored.}
+}
+\value{
+ The predict alpha coefficients.
+}
+\description{
+ Predict method for archetypal analysis
+}
+
Property changes on: pkg/man/predict.Rd
___________________________________________________________________
Added: svn:eol-style
+ native
More information about the Archetypes-commits
mailing list