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#######################################################################
# seriation - Infrastructure for seriation
# Copyright (C) 2011 Michael Hahsler, Christian Buchta and Kurt Hornik
#
# 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
# 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.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#' @rdname seriate
#' @export
seriate.dist <-
function(x,
method = "Spectral",
control = NULL,
rep = 1L,
...) {
if (rep > 1L)
return(seriate_rep(x, method, control, rep = rep, ...))
## add ... to control
control <- c(control, list(...))
## check x
if (anyNA(x)) stop("NAs not allowed in distance matrix x!")
if (any(x < 0)) stop("Negative distances not supported!")
if (!is.character(method) || (length(method) != 1L))
stop("Argument 'method' must be a character string.")
method <- get_seriation_method("dist", method)
if (!is.null(control$verbose) &&
control$verbose)
cat("Using seriation method: ", method$name, "\n",
method$description, "\n\n", sep = "")
tm <- system.time(order <- method$fun(x, control = control))
if (is.integer(order)) names(order) <- labels(x)[order]
if (!is.null(control$verbose) &&
control$verbose)
cat("Seriation took", tm[1] + tm[2], "sec\n\n")
ser_permutation(ser_permutation_vector(order, method = method$name))
}
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