A toolkit for working with phylogenetic data.
v0.24.0
mds.hpp
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1 #ifndef GENESIS_UTILS_MATH_MDS_H_
2 #define GENESIS_UTILS_MATH_MDS_H_
3 
4 /*
5  Genesis - A toolkit for working with phylogenetic data.
6  Copyright (C) 2014-2018 Lucas Czech and HITS gGmbH
7 
8  This program is free software: you can redistribute it and/or modify
9  it under the terms of the GNU General Public License as published by
10  the Free Software Foundation, either version 3 of the License, or
11  (at your option) any later version.
12 
13  This program is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  GNU General Public License for more details.
17 
18  You should have received a copy of the GNU General Public License
19  along with this program. If not, see <http://www.gnu.org/licenses/>.
20 
21  Contact:
22  Lucas Czech <lucas.czech@h-its.org>
23  Exelixis Lab, Heidelberg Institute for Theoretical Studies
24  Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
25 */
26 
35 
36 #include <vector>
37 
38 namespace genesis {
39 namespace utils {
40 
41 // ================================================================================================
42 // Settings for Functions
43 // ================================================================================================
44 
52 enum class MdsAlgorithm
53 {
60  kUcf,
61 
68  kSmacof
69 };
70 
71 // ================================================================================================
72 // Multi-Dimensional Scaling
73 // ================================================================================================
74 
84  Matrix<double> const& distances,
85  size_t dimensions = 2,
86  size_t iterations = 100,
88 );
89 
110  Matrix<double> const& distances,
111  Matrix<double> const& initial_values,
112  size_t dimensions = 2,
113  size_t iterations = 100,
114  MdsAlgorithm algorithm = MdsAlgorithm::kUcf
115 );
116 
117 } // namespace utils
118 } // namespace genesis
119 
120 #endif // include guard
Use the UCF implementation (recommended).
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
MdsAlgorithm
Choice of algorithm to use for Multi-Dimensional Scaling (MDS).
Definition: mds.hpp:52
Matrix< double > multi_dimensional_scaling(Matrix< double > const &distances, size_t dimensions, size_t iterations, MdsAlgorithm algorithm)
Multi-Dimensional Scaling (MDS).
Definition: mds.cpp:231
Use the SMACOF implementation.