R/dist.R

In BoutrosLab.plotting.general: Functions to Create Publication-Quality Plots

# The BoutrosLab.dist.overload package is copyright (c) 2012 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
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#  File src/library/stats/R/dist.R
#  Part of the R package, http://www.R-project.org
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
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#  A copy of the GNU General Public License is available at
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dist <- function(x, method="euclidean", diag=FALSE, upper=FALSE, p=2)
{
    ## account for possible spellings of euclid?an
    if(!is.na(pmatch(method, "euclidian")))
	method <- "euclidean"

    METHODS <- c("euclidean", "maximum",
		 "manhattan", "canberra", "binary", "minkowski", "jaccard")
    method <- pmatch(method, METHODS)
    if(is.na(method))
	stop("invalid distance method")
    if(method == -1)
	stop("ambiguous distance method")

    x <- as.matrix(x)
    N  <- nrow(x)
    if (!is.double(x)) storage.mode(x) <- "double"
    attrs <- if(method == 6L)
        list(Size = N, Labels =  dimnames(x)[[1L]], Diag = diag,
             Upper = upper, method = METHODS[method],
             p = p, call = match.call(), class = "dist")
    else
        list(Size = N, Labels =  dimnames(x)[[1L]], Diag = diag,
             Upper = upper, method = METHODS[method],
             call = match.call(), class = "dist")
    .Call("Cdist", x, method, attrs, p, PACKAGE = "BoutrosLab.plotting.general")
}