A toolkit for working with phylogenetic data.
v0.24.0
phylo_ilr.hpp
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1 #ifndef GENESIS_TREE_MASS_TREE_PHYLO_ILR_H_
2 #define GENESIS_TREE_MASS_TREE_PHYLO_ILR_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 
36 
37 #include <vector>
38 
39 namespace genesis {
40 namespace tree {
41 
42 // =================================================================================================
43 // Forward Declarations
44 // =================================================================================================
45 
46 class Tree;
47 using MassTree = Tree;
48 
49 // =================================================================================================
50 // Phylogenetic ILR Tranform
51 // =================================================================================================
52 
73 utils::Matrix<double> phylogenetic_ilr_transform(
74  BalanceData const& data,
75  bool reverse_signs = false
76 );
77 
87 utils::Matrix<double> edge_balances(
88  BalanceData const& data,
89  bool reverse_signs = false
90 );
91 
92 } // namespace tree
93 } // namespace genesis
94 
95 #endif // include guard
utils::Matrix< double > edge_balances(BalanceData const &data, bool reverse_signs)
Calculate edge balances using the Isometric Log Ratio transformation.
Definition: phylo_ilr.cpp:153
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
Tree MassTree
Alias for a Tree that stores masses on its TreeEdges.
utils::Matrix< double > phylogenetic_ilr_transform(BalanceData const &data, bool reverse_signs)
Calculate the Phylogenetic Isometric Log Ratio transformation.
Definition: phylo_ilr.cpp:62