R/Fclust.index.R

In fclust: Fuzzy Clustering

Fclust.index <- function (fclust.obj, index, alpha)
  {
    if ((missing(fclust.obj)) || (!inherits(fclust.obj,"fclust")))
      stop("An object of class fclust must be given")


    if(is.null(fclust.obj$D)){
      X <- fclust.obj$Xca
      isRelational = FALSE
    }else{
      X <- fclust.obj$D
      isRelational = TRUE
      cat("Xie and Beni index (XB) cannot be computed for relational data",fill=TRUE)
      }


    ind <- c("PC","PE","MPC","SIL","SIL.F","XB","ALL")
    U=fclust.obj$U
    H=fclust.obj$H
    m=fclust.obj$m
    lg=length(ind)
    if (missing(index))
    {
      indexN=lg
    }
    else
    {
      if (is.null(index))
      {
        indexN=lg
      }
      else
      {
        indexN=match(toupper(index),ind)
      }
    }
    if (any(is.na(indexN)))
    {
      indexN=lg
      cat("(At least one) no match is found: all the indices will be computed ",fill=TRUE)
    }
    index=indexN
    out.index=rep(0,lg-1)
    if (any(index==1) || any(index==lg))
      out.index[1]=PC(U)
    if (any(index==2) || any(index==lg))
      out.index[2]=PE(U)
    if (any(index==3) || any(index==lg))
      out.index[3]=MPC(U)
    if (any(index==4) || any(index==lg))
      out.index[4]=SIL(X,U = U,distance = isRelational)$sil
    if (any(index==5) || any(index==lg))
    {
      if (missing(alpha))
      {
        alpha=1
        cat("The default value alpha=1 has been set for computing SIL.F ",fill=TRUE)
      }
      if (!is.numeric(alpha))
      {
        alpha=1
        cat("The weighting coefficient alpha is not numeric: the default value alpha=1 will be used for computing SIL.F ",fill=TRUE)
      }
      if (alpha<0)
      {
        alpha=1
        cat("The number of clusters k must be non negative: the value alpha=1 will be used for computing SIL.F ",fill=TRUE)
      }
      out.index[5]=SIL.F(X,U = U,alpha = alpha,distance = isRelational)
    }
    if (any(index==6) || any(index==lg))
    {if(isRelational) {out.index[6] = NA}else{out.index[6]=XB(X,U,H,m)}
      names(out.index)=c("PC","PE","MPC","SIL","SIL.F","XB")
    }
    if (max(index)<lg)
      out.index=out.index[index]
    return(out.index)
  }