A toolkit for working with phylogenetic data.
v0.22.1
measures.hpp
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1 #ifndef GENESIS_PLACEMENT_FUNCTION_MEASURES_H_
2 #define GENESIS_PLACEMENT_FUNCTION_MEASURES_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 <cstddef>
37 #include <utility>
38 #include <vector>
39 
40 namespace genesis {
41 
42 // =================================================================================================
43 // Forward Declarations
44 // =================================================================================================
45 
46 namespace placement {
47 
48  class Sample;
49  class SampleSet;
50  class PlacementTreeEdgeData;
51  class PlacementTreeNodeData;
52  class Pquery;
53  class PqueryPlacement;
54  struct PqueryPlain;
55 
56 }
57 
58 namespace utils {
59 
60  template<typename T>
61  class Matrix;
62 
63  class Histogram;
64 
65 }
66 
67 namespace placement {
68 
69 // =================================================================================================
70 // Expected Distance between Placement Locations
71 // =================================================================================================
72 
85 double edpl( Pquery const& pquery, utils::Matrix<double> const& node_distances );
86 
95 std::vector<double> edpl( Sample const& sample, utils::Matrix<double> const& node_distances );
96 
107 double edpl( Sample const& sample, Pquery const& pquery );
108 
138 std::vector<double> edpl( Sample const& sample );
139 
140 // =================================================================================================
141 // Pairwise Distance
142 // =================================================================================================
143 
158 double pairwise_distance (
159  const Sample& smp_a,
160  const Sample& smp_b,
161  bool with_pendant_length = false
162 );
163 
164 // double closest_pair_distance (
165 // const Sample& smp_a,
166 // const Sample& smp_b,
167 // bool with_pendant_length = false
168 // );
169 
170 // =================================================================================================
171 // Variance
172 // =================================================================================================
173 
198 double variance (
199  const Sample& smp,
200  bool with_pendant_length = false
201 );
202 
203 } // namespace placement
204 } // namespace genesis
205 
206 #endif // include guard
double pairwise_distance(const Sample &smp_a, const Sample &smp_b, bool with_pendant_length)
Calculate the normalized pairwise distance between all placements of the two Samples.
Definition: measures.cpp:131
double variance(const Sample &smp, bool with_pendant_length)
Calculate the variance of the placements on a tree.
Definition: measures.cpp:232
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
double edpl(Pquery const &pquery, utils::Matrix< double > const &node_distances)
Calculate the EDPL uncertainty values for a Pquery.
Definition: measures.cpp:79