#######################################################################
# 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.
## QAP 2SUM seriation
seriate_dist_2SUM <- function(x, control = NULL) {
## param are passed on to QAP
do.call(qap::qap, c(list(
A = .A_2SUM(attr(x, "Size")),
B = 1 / (1 + as.matrix(x))
), control))
}
## QAP Linear seriation
seriate_dist_LS <- function(x, control = NULL) {
## param are passed on to QAP
do.call(qap::qap, c(list(A = .A_LS(attr(
x, "Size"
)),
B = as.matrix(x)), control))
}
## QAP Inertia
seriate_dist_Inertia <- function(x, control = NULL) {
## param are passed on to QAP
n <- attr(x, "Size")
## inertia uses the same A matrix as 2SUM
## we use n^2 since A needs to be positive
do.call(qap::qap, c(list(
A = n ^ 2 - .A_2SUM(n),
B = as.matrix(x)
), control))
}
## QAP BAR
.qap_bar_contr <- structure(list(
b = function(n)
max(1, floor(n * .2))
),
help = list(b = "bandwidth (default is 20%)"))
seriate_dist_BAR <- function(x, control = NULL) {
## param are passed on to QAP
if (is.null(control))
control <- .qap_bar_contr
if (is.null(control$b))
control$b <- .qap_bar_contr$b
.A_BAR <- function(n, b) {
b <- floor(b)
if (b < 1 || b >= n)
stop("b: needs to be 1<=b<n!")
A <- b + 1 - outer(
1:n,
1:n,
FUN = function(i, j)
abs(i - j)
)
A[A < 0] <- 0
A
}
n <- attr(x, "Size")
if (is.function(control$b))
b <- control$b(n)
else
b <- floor(control$b)
if (b < 1 || b > n)
stop("BAR bandwidth is not between 1 and n!")
control$b <- NULL
## inertia uses the same A matrix as 2SUM
do.call(qap::qap, c(list(A = .A_BAR(n, b = b),
B = as.matrix(x)), control))
}
set_seriation_method(
"dist",
"QAP_2SUM",
seriate_dist_2SUM,
"Quadratic assignment problem formulation for seriation solved using a simulated annealing solver to minimize the 2-Sum Problem criterion (Barnard, Pothen, and Simon 1993).",
randomized = TRUE,
optimizes = .opt("2SUM", "2-sum criterion")
)
set_seriation_method(
"dist",
"QAP_LS",
seriate_dist_LS,
"Quadratic assignment problem formulation for seriation solved using a simulated annealing solver to minimize the Linear Seriation Problem (LS) criterion (Hubert and Schultz 1976).",
randomized = TRUE,
optimizes = .opt("LS", "Linear seriation criterion")
)
set_seriation_method(
"dist",
"QAP_BAR",
seriate_dist_BAR,
"Quadratic assignment problem formulation for seriation solved using a simulated annealing solver to minimize the banded anti-Robinson form (Hahsler, 2017).",
.qap_bar_contr,
randomized = TRUE,
optimizes = .opt("BAR", "Banded anti-robinson form")
)
set_seriation_method(
"dist",
"QAP_Inertia",
seriate_dist_Inertia,
"Quadratic assignment problem formulation for seriation solved using a simulated annealing solver to minimize the Inertia criterion (Hahsler, 2017).",
randomized = TRUE,
optimizes = .opt("Inertia")
)
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