R/rankmatrix.R

In gdkrmr/coRanking: Co-Ranking Matrix

#' Rank matrix
#'
#' Replaces the elements of \eqn{X} with their rank in the column vector of
#' the distance matrix
#'
#' Each column vector in the distance matrix (or the distance matrix
#' computed from the input) is replaced by a vector indicating the
#' rank of the distance inside that vector.
#'
#' This is a computation step necessary for the co-ranking matrix and
#' provided mainly so that the user has the possibility to save
#' computation time.
#'
#' @param X data, dist object, or distance matrix
#' @param input type of input
#' @param use if 'C' uses the compiled library, else uses the native
#'     R code
#' @return returns a matrix of class \code{'rankmatrix'}
#' @author Guido Kraemer
#' @export
rankmatrix <- function(X, input = c("data", "dist"), use = "C") {
    input <- match.arg(input)
    if (input == "data") {
        dX <- euclidean(as.matrix(X), use)
        return(rankmatrix(dX, input = "dist", use))
    } else if (input == "dist") {
        dX <- as.matrix(X)
        nr <- dim(dX)[1]
        nc <- dim(dX)[2]

        if (nr != nc)
            stop("distance matrices must be square")
        if (!isSymmetric(dX))
            stop("distance matrices must be symmetric")
        if (!all(diag(dX) == 0))
            stop("diagonal of distance matrix must be 0")
        if (any(dX[-seq(1, nr ^ 2, nr + 1)] == 0))
            warning("0 outside of diagonal in distance matrix")

        if (use == "C") {
            return(rankmatrix_C(dX))
        } else {
            return(rankmatrix_R(dX))
        }
    }
    stop("input must be 'data' or 'dist'")
}