R/dist.R

In amap: Another Multidimensional Analysis Package

Dist <- function(x, method="euclidean", nbproc = 2, diag=FALSE, upper=FALSE)
{

  if(inherits(x,"exprSet"))
  {
      requireNamespace("Biobase")
      x <- Biobase::exprs(x)
  }
      
  ## account for possible spellings of euclidean
  if(!is.na(pmatch(method, "euclidian")))
	method <- "euclidean"

    METHODS <- c("euclidean", "maximum", "manhattan", "canberra",
                 "binary","pearson","correlation","spearman","kendall","abspearson","abscorrelation")
    method <- pmatch(method, METHODS)
    if(is.na(method))
	stop("invalid distance method")
    if(method == -1)
	stop("ambiguous distance method")

    N <- nrow(x <- as.matrix(x))
    d <- .C(C_R_distance,
	    x = as.double(x),
	    nr= N,
	    nc= ncol(x),
	    d = double(N*(N - 1)/2),
	    diag  = as.integer(FALSE),
	    method= as.integer(method),
            nbproc = as.integer(nbproc),
            ierr=as.integer(0),
            NAOK=TRUE,
            PACKAGE="amap"
            )$d
    attr(d, "Size") <- N
    attr(d, "Labels") <- dimnames(x)[[1]]
    attr(d, "Diag") <- diag
    attr(d, "Upper") <- upper
    attr(d, "method") <- METHODS[method]
    attr(d, "call") <- match.call()
    class(d) <- "dist"
    return(d)
}