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hclust2_result.cpp
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hclust2_result.cpp
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/* ************************************************************************* *
* This file is part of the `genie` package for R. *
* *
* Copyright 2015-2018 Marek Gagolewski, Maciej Bartoszuk, Anna Cena *
* *
* 'genie' 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 3 *
* of the License, or (at your option) any later version. *
* *
* 'genie' 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 'genie'. If not, see <http://www.gnu.org/licenses/>. *
* ************************************************************************* */
#include "hclust2_result.h"
using namespace grup;
using namespace Rcpp;
HClustResult::HClustResult(size_t n, Distance* dist, bool lite) :
curiter(0),
n(n),
links(n-1, 2), // this may be meaningless for some methods, do not return
merge(n-1, 2),
height(n-1),
order(n, NA_REAL),
labels(dist->getLabels()),
dist_method(dist->getDistMethod()),
lite(lite)
{
// no-op
}
void HClustResult::link(size_t i1, size_t i2, double d12)
{
STOPIFNOT(curiter < n-1);
links(curiter, 0) = (double)i1;
links(curiter, 1) = (double)i2;
height(curiter) = d12;
++curiter;
if (curiter == n-1 && !lite) {
generateMergeMatrix();
generateOrderVector();
}
}
void HClustResult::generateOrderVector()
{
std::vector< std::list<double> > relord(n+1);
size_t clusterNumber = 1;
for (size_t k=0; k<n-1; ++k, ++clusterNumber) {
double i = merge(k, 0);
if (i < 0)
relord[clusterNumber].push_back(-i);
else
relord[clusterNumber].splice(relord[clusterNumber].end(), relord[(size_t)i]);
double j = merge(k, 1);
if (j < 0)
relord[clusterNumber].push_back(-j);
else
relord[clusterNumber].splice(relord[clusterNumber].end(), relord[(size_t)j]);
}
STOPIFNOT(relord[n-1].size() == n);
size_t k = 0;
for (std::list<double>::iterator it = relord[n-1].begin();
it != relord[n-1].end(); ++it) {
order[k++] = (*it);
}
}
void HClustResult::generateMergeMatrix()
{
STOPIFNOT(curiter == n-1);
std::vector<size_t> elements(n+1, 0);
std::vector<size_t> parents(n+1, 0);
size_t clusterNumber = 1;
for (size_t k=0; k<n-1; ++k, ++clusterNumber) {
size_t i = (size_t)links(k, 0) + 1;
size_t j = (size_t)links(k, 1) + 1;
size_t si = elements[i];
size_t sj = elements[j];
elements[i] = clusterNumber;
elements[j] = clusterNumber;
if (si == 0)
merge(k, 0) = -(double)i;
else {
while (parents[si] != 0) {
size_t sinew = parents[si];
parents[si] = clusterNumber;
si = sinew;
}
if (si != 0) parents[si] = clusterNumber;
merge(k,0) = (double)si;
}
if (sj == 0)
merge(k, 1) = -(double)j;
else {
while (parents[sj] != 0) {
size_t sjnew = parents[sj];
parents[sj] = clusterNumber;
sj = sjnew;
}
if (sj != 0) parents[sj] = clusterNumber;
merge(k,1) = (double)sj;
}
if (merge(k, 0) < 0) {
if (merge(k, 1) < 0 && merge(k, 0) < merge(k, 1)) std::swap(merge(k, 0), merge(k, 1));
}
else {
if (merge(k, 0) > merge(k, 1)) std::swap(merge(k, 0), merge(k, 1));
}
}
}
List HClustResult::toR(
const HClustStats& hclustStats,
const HClustOptions& hclustOptions,
const DistanceStats& distStats)
{
MESSAGE_2("[%010.3f] generating output matrix\n", clock()/(float)CLOCKS_PER_SEC);
List result = List::create(
_["merge"] = merge,
_["height"] = height,
_["order"] = order,
_["labels"] = labels,
_["call"] = R_NilValue,
_["method"] = R_NilValue,
_["dist.method"] = dist_method,
_["links"] = links,
_["stats"] = List::create(
_["method"] = hclustStats.toR(),
_["distance"] = distStats.toR()
),
_["control"] = List::create(
_["method"] = hclustOptions.toR()
)
);
result.attr("class") = "hclust";
return result;
}