R/coranking.R

In gdkrmr/coRanking: Co-Ranking Matrix

#' Co-Ranking Matrix
#'
#' Calculate the co-ranking matrix to assess the quality of a
#' diminsionality reduction.
#'
#' Calculate the coranking matrix, to assess the quality of a dimensionality
#' reduction. \code{Xi} is input in high dimensions, \code{X} is input in low
#' dimensions the type of input is given in \code{input_Xi} and \code{input_X},
#' they can be one of \code{c('data', 'dist', 'rank')}.
#'
#' @param Xi high dimensional data
#' @param X low dimensional data
#' @param input_Xi type of input of Xi (see. details)
#' @param input_X type of input of X (see. details)
#' @param use \code{R} or \code{C} backend
#' @return a matrix of class \code{'coranking'}
#' @author Guido Kraemer
#' @seealso \code{\link{rankmatrix}}
#' @export
coranking <- function(Xi, X,
                      input_Xi = c("data", "dist", "rank"),
                      input_X = input_Xi,
                      use = "C") {

  input_Xi <- match.arg(input_Xi, c("data", "dist", "rank"))
  input_X <- match.arg(input_X, c("data", "dist", "rank"))

  if (input_Xi == "data" || input_Xi == "dist")
    rXi <- rankmatrix(Xi, input = input_Xi,  use = use)
  else
    rXi <- Xi


  if (input_X == "data" || input_X == "dist")
    rX <- rankmatrix(X, input = input_X, use = use)
  else
    rX <- X


  if (!all.equal(dim(rXi)[1], dim(rXi)[2], dim(rX)[1], dim(rX)[2]))
    stop("input must be the same size and square matrices")
  if (!is.integer(rXi) || !is.integer(rX))
    stop("input must be integer")

  if (use == "C") {
    return(coranking_C(rXi, rX))
  } else {
    return(coranking_R(rXi, rX))
  }
}