R/PAMclustering.R

In FCPS: Fundamental Clustering Problems Suite

PAMclustering=PAMClustering=function(DataOrDistances,ClusterNo,PlotIt=FALSE,Standardization=TRUE,Data,...){
  # INPUT
  # Data[1:n,1:d]     Data set with n observations and d features
  # ClusterNo         Number of clusters to search for
  #
  # OPTIONAL
  # PlotIt            Boolean. Decision to plot or not
  # Standardization   Boolean.
  # 
  # OUTPUT
  # Cls[1:n]          Clustering of data
  # Object            Object of cluster::pam algorithm
  #
  # Author: MT, 04/2018
  if (!requireNamespace('cluster',quietly = TRUE)) {
    message(
      'Subordinate clustering package (cluster) is missing. No computations are performed.
            Please install the package which is defined in "Suggests".'
    )
    return(
      list(
        Cls = rep(1, nrow(DataOrDistances)),
        Object = "Subordinate clustering package (cluster) is missing.
                Please install the package which is defined in 'Suggests'."
      )
    )
  }
  
  if(missing(DataOrDistances)){
    DataOrDistances=Data
  }
  if(Standardization==1) Standardization=TRUE
  if(Standardization==0) Standardization=FALSE
      if (isSymmetric(unname(DataOrDistances))) {
      Input = as.dist(DataOrDistances)
      AnzVar = ncol(DataOrDistances)
      AnzData = nrow(DataOrDistances)
	  diss =TRUE
    }else{
	  Input=DataOrDistances
	  diss =FALSE
    }
	
  pam=cluster::pam(x=Input,k=ClusterNo,diss=diss,stand=Standardization,...)
  Cls=pam$clustering
  if(!is.null(rownames(DataOrDistances)))
    names(Cls)=rownames(DataOrDistances)
  else
    names(Cls)=1:nrow(DataOrDistances)
  
  if(PlotIt){
		ClusterPlotMDS(DataOrDistances,Cls)
  }
  Cls=ClusterRename(Cls,DataOrDistances)
  return(list(Cls=Cls,Object=pam))
}