R/global.R

In MixAll: Clustering and Classification using Model-Based Mixture Models

#-----------------------------------------------------------------------
#     Copyright (C) 2012-2016  Serge Iovleff, University Lille 1, Inria
#
#    This program is free software; you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as
#    published by the Free Software Foundation; either version 2 of the
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#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
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#    License along with this program; if not, write to the
#    Free Software Foundation, Inc.,
#    59 Temple Place,
#    Suite 330,
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#    USA
#
#    Contact : S..._Dot_I..._At_stkpp_Dot_org (see copyright for ...)
#
#-----------------------------------------------------------------------

#' Return the missing values of a component or a cluster class.
#'
#' The missing methods allow the user to get the imputed mssing
#' values from a mixture model.
#'
#' @param x an object that can return the imputed missing values
#'
#' @return A matrix with three columns (row index, column index, value)
#'
#' @name missingValues
#' @docType methods
#' @rdname missingValues-methods
#'
#' @examples
#' \dontrun{
#' ## add 10 missing values as random
#' data(geyser)
#' x = as.matrix(geyser); n <- nrow(x); p <- ncol(x);
#' indexes <- matrix(c(round(runif(5,1,n)), round(runif(5,1,p))), ncol=2);
#' x[indexes] <- NA;
#' ## estimate model (using fast strategy, results may be misleading)
#' model <- clusterDiagGaussian(data=x, nbCluster=2:3, strategy = clusterFastStrategy())
#' missingValues(model)
#' }
#' 
setGeneric(
    name = "missingValues",
    function(x)
    { standardGeneric("missingValues")}
)

#' Extract parts of a MixAll S4 class
#'
#' @param x object from which to extract element(s) or in which to replace element(s).
#' @param i the name of the element we want to extract or replace.
#' @param j if the element designing by i is complex, j specifying elements to extract or replace.
#' @param drop For matrices and arrays.  If TRUE the result is coerced to the lowest
#' possible dimension (see the examples).  This only works for extracting elements,
#' not for the replacement.  See drop for further details.
#' @param value	typically an array-like R object of a similar class as the element
#' of x we want to replace.
#' @name [
#' @aliases Extract
#' @docType methods
#' @rdname extract-methods
#'
NULL

#' Print a MixAll S4 class to standard output.
#'
#' @param x a MixAll object: a \code{\linkS4class{ClusterStrategy}},
#' a \code{\linkS4class{ClusterInit}} or a \code{\linkS4class{ClusterAlgo}}.
#' @param ... further arguments passed to or from other methods
#'
#' @return NULL. Prints to standard out.
#'
#' @name print
#' @rdname print-methods
#' @docType methods
#'
#' @seealso \code{\link{print}}
#' @examples
#'   ## for cluster strategy
#'   strategy <- clusterStrategy()
#'   print(strategy)
#'   ## for cluster init
#'   init <- clusterInit()
#'   print(init)
#'   ## for cluster algo
#'   algo <- clusterAlgo()
#'   print(algo)
#'
NULL

#' Show description of a MixAll S4 class to standard output.
#'
#' @param object a MixAll object: a \code{\linkS4class{ClusterStrategy}},
#' a \code{\linkS4class{ClusterInit}} or a \code{\linkS4class{ClusterAlgo}}.
#'
#' @return NULL. Prints to standard out.
#'
#' @name show
#' @docType methods
#' @rdname show-methods
#'
#' @seealso \code{\link{show}}
#' @examples
#'   ## for strategy
#'   strategy <- clusterStrategy()
#'   show(strategy)
#'   ## for cluster init
#'   init <- clusterInit()
#'   show(init)
#'   ## for cluster algo
#'   algo <- clusterAlgo()
#'   show(algo)
#' 
NULL


#' Produce summary of a MixAll S4 class.
#'
#' @param object any cluster model deriving from a \code{\linkS4class{IClusterModel}}
#' or \code{\linkS4class{IClusterComponent}} object.
#' @param ... further arguments passed to or from other methods
#'
#' @return NULL. Summaries to standard out.
#'
#' @name summary
#' @docType methods
#' @rdname summary-methods
#'
NULL