[Archetypes-commits] r50 - in pkg: . R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 26 10:23:36 CEST 2011
Author: manuel
Date: 2011-10-26 10:23:25 +0200 (Wed, 26 Oct 2011)
New Revision: 50
Added:
pkg/R/generics.R
Modified:
pkg/DESCRIPTION
pkg/R/archetypes-class.R
pkg/R/archetypes-kit-blocks.R
pkg/R/archetypes-kit.R
pkg/R/archetypes-panorama.R
pkg/R/archetypes-pcplot.R
pkg/R/archetypes-robust.R
pkg/R/archetypes-step.R
pkg/R/archetypes-weighted.R
pkg/R/memento.R
pkg/R/pcplot.R
pkg/R/skeletonplot.R
Log:
...
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/DESCRIPTION 2011-10-26 08:23:25 UTC (rev 50)
@@ -1,7 +1,7 @@
Package: archetypes
Type: Package
Title: Archetypal Analysis
-Version: 2.1
+Version: 2.1-0
Date: 2011-10-25
Depends:
methods,
@@ -25,6 +25,7 @@
Revision: 44
Collate:
'archetypes-barplot.R'
+ 'generics.R'
'archetypes-class.R'
'archetypes-kit-blocks.R'
'archetypes-kit.R'
@@ -39,4 +40,3 @@
'archetypes-xyplot.R'
'memento.R'
'skeletonplot.R'
- 'generics.R'
Modified: pkg/R/archetypes-class.R
===================================================================
--- pkg/R/archetypes-class.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-class.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -1,6 +1,9 @@
+#' @include generics.R
+{}
-#' Archetypes object constructor and methods
+
+#' Archetypes object constructor
#'
#' @param object The archetypes; a \eqn{p \times m} matrix, see
#' \code{\link{parameters}}.
@@ -52,10 +55,9 @@
-setOldClass('archetypes')
+setOldClass(c("archetypes"))
-
#' @S3method print archetypes
print.archetypes <- function(x, full = TRUE, ...) {
if ( full ) {
@@ -93,6 +95,9 @@
#' @param ... Ignored.
#' @return Matrix with \eqn{k} archetypes.
#'
+#' @aliases parameters-methods
+#' @aliases parameters,archetypes-method
+#'
#' @importFrom modeltools parameters
#' @exportMethod parameters
setMethod('parameters', signature = c(object = 'archetypes'),
Modified: pkg/R/archetypes-kit-blocks.R
===================================================================
--- pkg/R/archetypes-kit-blocks.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-kit-blocks.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -389,7 +389,7 @@
### Archetypes family: ###############################################
-#' Archetypes family constructor.
+#' Archetypes family constructor
#'
#' This function returns a problem solving block for each of the
#' different conceptual parts of the algorithm.
@@ -397,8 +397,11 @@
#' @param which The kind of archetypes family.
#' @param ... Exchange predefined family blocks with self-defined
#' functions.
+#'
#' @return A list containing a function for each of the different parts.
-#' @seealso \code{\link{archetypes}}
+#'
+#' @family archetypes
+#'
#' @export
archetypesFamily <- function(which = c('original', 'weighted', 'robust'), ...) {
Modified: pkg/R/archetypes-kit.R
===================================================================
--- pkg/R/archetypes-kit.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-kit.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -1,3 +1,4 @@
+#' @include generics.R
#' @include archetypes-kit-blocks.R
#' @include archetypes-class.R
{}
Modified: pkg/R/archetypes-panorama.R
===================================================================
--- pkg/R/archetypes-panorama.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-panorama.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -1,16 +1,6 @@
-#' Panorama plot.
-#' @param object An object.
-#' @param ... Further arguments.
-#' @return Undefined.
-#' @export
-panorama <- function(object, ...) {
- UseMethod('panorama')
-}
-
-
#' Panorma plot for archetypes.
#' @param object An \code{\link{archetypes}}-related object.
#' @param data A matrix or data frame.
Modified: pkg/R/archetypes-pcplot.R
===================================================================
--- pkg/R/archetypes-pcplot.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-pcplot.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -29,7 +29,7 @@
lines.pcplot(data[chull,], data,
col=chull.col, lwd=chull.lwd, lty=chull.lty, ...)
- lines.pcplot(atypes(x), data,
+ lines.pcplot(parameters(x), data,
col=atypes.col, lwd=atypes.lwd, lty=atypes.lty, ...)
}
Modified: pkg/R/archetypes-robust.R
===================================================================
--- pkg/R/archetypes-robust.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-robust.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -5,10 +5,11 @@
-#' Robust archetypes.
+#' Robust archetypes
#'
#' @inheritParams archetypes
-#' @param familyBlocks Exchange predefined family blocks.
+#' @param familyBlocks Exchange predefined family blocks; see
+#' \code{\link{archetypesFamily}}.
#'
#' @return An object of class \code{robustArchetypes} and
#' \code{\link{as.archetypes}}.
@@ -35,5 +36,4 @@
-#setOldClass("robustArchetypes")
-#setIs("robustArchetypes", "archetypes")
+setOldClass(c("robustArchetypes", "archetypes"))
Modified: pkg/R/archetypes-step.R
===================================================================
--- pkg/R/archetypes-step.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-step.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -116,6 +116,9 @@
+#' @aliases parameters,stepArchetypes-method
+#' @rdname parameters
+#' @importFrom modeltools parameters
#' @exportMethod parameters
setMethod('parameters', signature = c(object = 'stepArchetypes'),
function(object, ...) {
@@ -176,6 +179,8 @@
+#' @aliases parameters,repArchetypes-method
+#' @rdname parameters
#' @importFrom modeltools parameters
#' @exportMethod parameters
setMethod('parameters', signature = signature(object = 'repArchetypes'),
Modified: pkg/R/archetypes-weighted.R
===================================================================
--- pkg/R/archetypes-weighted.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/archetypes-weighted.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -9,7 +9,8 @@
#'
#' @inheritParams archetypes
#' @param weights Data weights matrix.
-#' @param familyBlocks Exchange predefined family blocks.
+#' @param familyBlocks Exchange predefined family blocks; see
+#' \code{\link{archetypesFamily}}.
#'
#' @return An object of class \code{weightedArchetypes} and
#' \code{\link{as.archetypes}}.
@@ -36,6 +37,4 @@
-#setOldClass("weightedArchetypes")
-#setIs("weightedArchetypes", "archetypes")
-
+setOldClass(c("weightedArchetypes", "archetypes"))
Added: pkg/R/generics.R
===================================================================
--- pkg/R/generics.R (rev 0)
+++ pkg/R/generics.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -0,0 +1,59 @@
+
+#' Defined generics
+#'
+#' Generics defined by the archetypes package.
+#'
+#' @param object An object
+#' @param ... Futher arguments
+#' @rdname archetypes-generics
+#'
+#' @export
+rss <- function(object, ...) {
+ UseMethod('rss')
+}
+
+
+
+#' Return number of parameters
+#'
+#' @rdname archetypes-generics
+#'
+#' @export
+nparameters <- function(object, ...) {
+ UseMethod('nparameters')
+}
+
+
+
+
+#' Return best model
+#'
+#' @rdname archetypes-generics
+#'
+#' @export
+bestModel <- function(object, ...) {
+ UseMethod('bestModel')
+}
+
+
+
+#' Panorama
+#'
+#' @rdname archetypes-generics
+#'
+#' @export
+panorama <- function(object, ...) {
+ UseMethod('panorama')
+}
+
+
+
+#' Parallel coordinates plot
+#'
+#' @param x An object.
+#' @rdname archetypes-generics
+#'
+#' @export
+pcplot <- function(x, ...) {
+ UseMethod('pcplot')
+}
Property changes on: pkg/R/generics.R
___________________________________________________________________
Added: svn:keywords
+ Date Revision Author URL Id Header
Added: svn:eol-style
+ native
Modified: pkg/R/memento.R
===================================================================
--- pkg/R/memento.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/memento.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -6,8 +6,9 @@
#'
#' @param i The number of the state.
#' @param state The state to save.
+#'
#' @return Memento environment.
-#' @export
+#'
#' @examples
#' \dontrun{
#' m <- new.memento()
@@ -16,6 +17,9 @@
#' m$get(i)
#' }
#' @aliases memento
+#' @rdname memento
+#'
+#' @export
new.memento <- function() {
memento <- new.env(parent = emptyenv())
Modified: pkg/R/pcplot.R
===================================================================
--- pkg/R/pcplot.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/pcplot.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -1,14 +1,8 @@
+#' @include generics.R
+{}
-#' Parallel coordinates plot.
-#' @param x An object.
-#' @param ... Further arguments.
-#' @export
-pcplot <- function(x, ...) {
- UseMethod('pcplot')
-}
-
#' Default parallel coordinates plot.
#'
#' Code copied from function \code{\link[MASS]{parcoord}} of package
Modified: pkg/R/skeletonplot.R
===================================================================
--- pkg/R/skeletonplot.R 2011-10-25 15:27:51 UTC (rev 49)
+++ pkg/R/skeletonplot.R 2011-10-26 08:23:25 UTC (rev 50)
@@ -137,9 +137,9 @@
#' measurements available in data set \code{\link{skel}}.
#'
#' @return Generic skeleton instance.
+#' @rdname skeletonplot
+#'
#' @export
-#' @usage
-#' jd()
jd <- function() {
jd <- rbind(c(AnkleDiam=13.9, KneeDiam=18.8, WristDiam=10.5, Bitro=32.0,
Biil=27.8, ElbowDiam=13.4, ChestDiam=28.0, ChestDp=15,
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