balances.hpp

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#ifndef GENESIS_TREE_MASS_TREE_BALANCES_H_
#define GENESIS_TREE_MASS_TREE_BALANCES_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 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/tree/tree.hpp"
#include "genesis/utils/containers/matrix.hpp"

#include <vector>
#include <unordered_set>

namespace genesis {
namespace tree {

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

using MassTree = Tree;

// =================================================================================================
//     Balance Settings
// =================================================================================================

struct BalanceSettings
{
    enum class WeightTendency
    {
        kNone,

        kMedian,

        kArithmeticMean,

        kGeometricMean
    };

    enum class WeightNorm
    {
        kNone,

        kManhattan,

        kEuclidean,

        kMaximum,

        kAitchison
    };

    WeightTendency tendency = WeightTendency::kGeometricMean;

    WeightNorm     norm     = WeightNorm::kEuclidean;

    double pseudo_count_summand_all = 1.0;

    double pseudo_count_summand_zeros = 0.0;
};

// =================================================================================================
//     Balance Data
// =================================================================================================

struct BalanceData
{
    Tree tree;

    utils::Matrix<double> edge_masses;

    utils::Matrix<double> raw_edge_masses;

    std::vector<double> taxon_weights;
};

// =================================================================================================
//     Balances and Weights Calculations
// =================================================================================================

BalanceData mass_balance_data(
    std::vector<MassTree> const& trees,
    BalanceSettings settings = {}
);

BalanceData mass_balance_data(
    MassTree const& tree,
    BalanceSettings settings = {}
);

std::vector<double> mass_balance(
    BalanceData const& data,
    std::unordered_set<size_t> const& numerator_edge_indices,
    std::unordered_set<size_t> const& denominator_edge_indices
);

double mass_balance(
    BalanceData const& data,
    std::unordered_set<size_t> const& numerator_edge_indices,
    std::unordered_set<size_t> const& denominator_edge_indices,
    size_t tree_index
);

} // namespace tree
} // namespace genesis

#endif // include guard