A toolkit for working with phylogenetic data.
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tree/mass_tree/emd.hpp
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1 #ifndef GENESIS_TREE_MASS_TREE_EMD_H_
2 #define GENESIS_TREE_MASS_TREE_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 <cstddef>
35 #include <utility>
36 #include <vector>
37 
38 namespace genesis {
39 
40 // =================================================================================================
41 // Forward Declarations
42 // =================================================================================================
43 
44 namespace utils {
45 
46  template<typename T>
47  class Matrix;
48 
49 }
50 
51 namespace tree {
52 
53  class Tree;
54  class TreeNode;
55  class TreeEdge;
56 
57  using MassTree = Tree;
58 
59 }
60 
61 namespace tree {
62 
63 // =================================================================================================
64 // Earth Movers Distance
65 // =================================================================================================
66 
115 double earth_movers_distance( MassTree const& lhs, MassTree const& rhs, double p = 1.0 );
116 
124 utils::Matrix<double> earth_movers_distance( std::vector<MassTree> const& trees, double p = 1.0 );
125 
150 std::pair<double, double> earth_movers_distance( MassTree const& tree, double p = 1.0 );
151 
152 } // namespace tree
153 } // namespace genesis
154 
155 #endif // include guard
Tree MassTree
Alias for a Tree that stores masses on its TreeEdges.
double earth_movers_distance(MassTree const &lhs, MassTree const &rhs, double const p)
Calculate the earth mover's distance of two distributions of masses on a given Tree.