epca.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_EPCA_H_
#define GENESIS_PLACEMENT_FUNCTION_EPCA_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2018 Lucas Czech and HITS gGmbH

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/

#include "genesis/placement/placement_tree.hpp"
#include "genesis/utils/containers/matrix.hpp"

#include <vector>

namespace genesis {

// =================================================================================================
//     Forward Declarations
// =================================================================================================

namespace tree {

    class Tree;

    class CommonNodeData;
    class CommonEdgeData;

    using CommonTree = Tree;
}

namespace placement {
    class PlacementEdgeData;
    class PlacementNodeData;

    class Sample;
    class SampleSet;
}

namespace placement {

// =================================================================================================
//     Edge PCA
// =================================================================================================

struct EpcaData
{
    std::vector<double>   eigenvalues;
    utils::Matrix<double> eigenvectors;
    utils::Matrix<double> projection;
    std::vector<size_t>   edge_indices;
};

std::vector<double> epca_imbalance_vector( Sample const& sample, bool normalize = true );

utils::Matrix<double> epca_imbalance_matrix(
    SampleSet const& samples,
    bool include_leaves = false,
    bool normalize = true
);

void epca_splitify_transform(
    utils::Matrix<double>& imbalance_matrix,
    double                 kappa = 1.0
);

EpcaData epca(
    SampleSet const& samples,
    double kappa      = 1.0,
    double epsilon    = 1e-5,
    size_t components = 0
);

} // namespace placement
} // namespace genesis

#endif // include guard