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#' @include coclusterStrategy.R
#' @include optionclasses.R
#'
NULL
#' Co-Clustering function.
#'
#' This function performs Co-Clustering (simultaneous clustering of rows and columns )
#' for Contingency data-sets using latent block models.It can also be used to
#' perform semi-supervised co-clustering.
#'
#' @param data Input data as matrix (or list containing data matrix, numeric vector for row effects and numeric
#' vector column effects in case of contingency data with known row and column effects.)
#' @param semisupervised Boolean value specifying whether to perform semi-supervised
#' co-clustering or not. Make sure to provide row and/or column labels if
#' specified value is true. The default value is false.
#' @param rowlabels Integer Vector specifying the class of rows. The class number starts from zero. Provide -1 for unknown row class.
#' @param collabels Integer Vector specifying the class of columns. The class number starts from zero. Provide -1 for unknown column class.
#' @param model This is the name of model. The following models exists for Poisson data:
#' \tabular{rlll}{
#' pik_rhol_unknown(default) \tab contingency \tab unequal \tab N.A \cr
#' pi_rho_unknown \tab contingency \tab equal \tab N.A \cr
#' pik_rhol_known \tab contingency \tab unequal \tab N.A \cr
#' pi_rho_known \tab contingency \tab equal \tab N.A \cr
#' }
#'
#' @param nbcocluster Integer vector specifying the number of row and column clusters respectively.
#' @param strategy Object of class \code{\linkS4class{strategy}}.
#' @param nbCore number of thread to use (OpenMP must be available), 0 for all cores. Default value is 1.
#'
#' @return Return an object of \code{\linkS4class{BinaryOptions}} or \code{\linkS4class{ContingencyOptions}}
#' or \code{\linkS4class{ContinuousOptions}} depending on whether the data-type is Binary, Contingency or Continuous
#' respectively.
#'
# @export
#'
# @exportPattern "^[[:alpha:]]+"
# @useDynLib RCocluster
#'
#' @examples
#'
#' ## Simple example with simulated contingency data
#' ## load data
#' data(contingencydataunknown)
#' ## usage of coclusterContingency function in its most simplest form
#' strategy = coclusterStrategy( nbinititerations = 5, nbxem = 2, nbiterations_int = 2
#' , nbiterationsxem = 10, nbiterationsXEM = 100, epsilonXEM=1e-5)
#' out<-coclusterContingency( contingencydataunknown, nbcocluster=c(2,3), strategy = strategy)
#' ## Summarize the output results
#' summary(out)
#' ## Plot the original and Co-clustered data
#' plot(out)
#'
coclusterContingency<-function( data, semisupervised = FALSE
, rowlabels = integer(0), collabels = integer(0)
, model = NULL, nbcocluster, strategy = coclusterStrategy()
, nbCore = 1)
{
#Check for data
if(missing(data)){ stop("Data is missing.")}
if(!is.list(data))
{
if(!is.matrix(data)) { stop("Data should be matrix.")}
dimData = dim(data)
}
else
{
if(!is.matrix(data[[1]])) { stop("Data should be matrix.")}
if(!is.numeric(data[[2]])||!is.numeric(data[[3]]))
{ stop("Row/Column effects should be numeric vectors.")}
if(length(data[[2]])!=dim(data[[1]])[1]||length(data[[3]])!=dim(data[[1]])[2])
{ stop("Dimension mismatch in Row/column effects and Data.")}
dimData = dim(data[[1]])
}
#check for row and column labels
if (semisupervised)
{
if(missing(rowlabels)&&missing(collabels))
stop("Missing row and column labels. At-least one should be provided to perform semi-supervised Co-clustering.")
if(!missing(rowlabels)&&!is.numeric(rowlabels))
stop("Row labels should be a numeric vector.")
if(!missing(collabels)&&!is.numeric(collabels))
stop("Column labels should be a numeric vector.")
if(missing(rowlabels)) rowlabels = rep(-1,dimData[1])
else if(missing(collabels)) collabels = rep(-1,dimData[2])
if(dimData[1]!=length(rowlabels))
stop("rowlabels length does not match number of rows in data (also ensure to put -1 in unknown labels)")
if(dimData[2]!=length(collabels))
stop("collabels length does not match number of columns in data (also ensure to put -1 in unknown labels)")
}
#check for number of coclusters
if(missing(nbcocluster)) { stop("Mention number of CoClusters.")}
if(dimData[1]<nbcocluster[1]){ stop("Number of Row clusters exceeds numbers of rows.")}
if(dimData[2]<nbcocluster[2]){ stop("Number of Column clusters exceeds numbers of columns.")}
if(nbcocluster[1]<1 || nbcocluster[2]<1) { stop("Number of cluster must be at least 1.")}
#check for Algorithm name (and make it compatible with version 1)
if(strategy@algo=="XEMStrategy")
{
warning("The algorithm 'XEMStrategy' is renamed as BEM!")
strategy@algo == "BEM"
}
else if(strategy@algo == "XCEMStrategy")
{
warning("The algorithm 'XCEMStrategy' is renamed as BCEM!")
strategy@algo = "BCEM"
}
else if(strategy@algo!="BEM" && strategy@algo!="BCEM" && strategy@algo!="BSEM" )
{
stop("Incorrect Algorithm, Valide algorithms are: BEM, BCEM, BSEM")
}
#check for stopping criteria
if(strategy@stopcriteria!="Parameter" && strategy@stopcriteria!="Likelihood")
stop("Incorrect stopping criteria, Valid stopping criterians are: Parameter, Likelihood")
#check for datatype and models and create input object to be passed in .Call function.
if(is.null(model) && !is.list(data)){ model = "pik_rhol_unknown"}
else if(is.null(model) && is.list(data)) { model = "pik_rhol_known"}
else
{
if(model!="pik_rhol_unknown" && model!="pik_rhol_known" &&
model!="pi_rho_unknown" && model!="pi_rho_known")
{
stop("Incorrect Model, Valid Contingency models are:pik_rhol_unknown, pik_rhol_known, pi_rho_unknown, pi_rho_known")
}
}
if((model=="pi_rho_known"||model=="pik_rhol_known")&& (length(data)!=3))
{stop("Missing Row/Column effects.")}
if(length(strategy@initmethod)==0){ strategy@initmethod = "emInitStep"}
## {
## if((model=="pi_rho_known"||model=="pik_rhol_known"))
## { strategy@initmethod = "emInitStep"}
## else
## { strategy@initmethod = "emInitStep"}
## }
## else
## {
## if(strategy@initmethod!="randomInit"&&(model=="pi_rho_known"||model=="pik_rhol_known"))
## { stop("Incorrect initialization method, valid method(s) are: randomInit")}
## else if((strategy@initmethod!="cemInitStep" && strategy@initmethod!="emInitStep")&&(model=="pi_rho_unknown"||model=="pik_rhol_unknown"))
## stop("Incorrect initialization method, valid method(s) are: cemInitStep, emInitStep")
## }
# check nbCore
if(!is.numeric(nbCore) && length(nbCore) != 1) stop("nbCore must be an integer")
# check options
if(!is.list(data))
inpobj<-new( "ContingencyOptions", data = data
, semisupervised = semisupervised
, rowlabels = rowlabels, collabels = collabels
, datatype = "contingency", model = model, nbcocluster = nbcocluster, strategy = strategy)
else
inpobj<-new( "ContingencyOptions",data = data[[1]]
, datamui=data[[2]],datanuj=data[[3]]
, semisupervised = semisupervised
, rowlabels = rowlabels, collabels = collabels
, datatype = "contingency", model = model, nbcocluster = nbcocluster, strategy = strategy)
.Call("CoClustmain",inpobj, nbCore,PACKAGE = "blockcluster")
cat(inpobj@message,"\n")
return(inpobj)
}
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