A toolkit for working with phylogenetic data.
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placement/function/emd.hpp
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1 #ifndef GENESIS_PLACEMENT_FUNCTION_EMD_H_
2 #define GENESIS_PLACEMENT_FUNCTION_EMD_H_
3 
4 /*
5  Genesis - A toolkit for working with phylogenetic data.
6  Copyright (C) 2014-2017 Lucas Czech
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 
34 #include <utility>
35 #include <vector>
36 
37 namespace genesis {
38 
39 // =================================================================================================
40 // Forward Declarations
41 // =================================================================================================
42 
43 namespace placement {
44 
45  class Sample;
46  class SampleSet;
47 
48 }
49 
50 namespace utils {
51 
52  template<typename T>
53  class Matrix;
54 
55 }
56 
57 namespace placement {
58 
59 // =================================================================================================
60 // Earth Movers Distance
61 // =================================================================================================
62 
97 double earth_movers_distance (
98  Sample const& lhs,
99  Sample const& rhs,
100  double const p = 1.0,
101  bool const with_pendant_length = false
102 );
103 
117  SampleSet const& sample_set,
118  double const p = 1.0,
119  bool const with_pendant_length = false
120 );
121 
122 } // namespace placement
123 } // namespace genesis
124 
125 #endif // include guard
double earth_movers_distance(Sample const &lhs, Sample const &rhs, double const p, bool const with_pendant_length)
Calculate the earth mover's distance between two Samples.