epca.cpp File Reference

#include "genesis/placement/function/epca.hpp"
#include "genesis/placement/function/functions.hpp"
#include "genesis/placement/function/helper.hpp"
#include "genesis/placement/function/masses.hpp"
#include "genesis/placement/function/sample_set.hpp"
#include "genesis/tree/function/functions.hpp"
#include "genesis/tree/iterator/postorder.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/containers/matrix/operators.hpp"
#include "genesis/utils/core/std.hpp"
#include "genesis/utils/math/common.hpp"
#include "genesis/utils/math/matrix.hpp"
#include "genesis/utils/math/pca.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <numeric>
#include <stdexcept>
#include <vector>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::placement

Functions
EpcaData	epca (SampleSet const &samples, double kappa=1.0, double epsilon=1e-5, size_t components=0)
	Perform EdgePCA on a SampleSet. More...
utils::Matrix< double >	epca_imbalance_matrix (SampleSet const &samples, bool include_leaves=false, bool normalize=true)
	Calculate the imbalance matrix of placment mass for all Samples in a SampleSet. More...
std::vector< double >	epca_imbalance_vector (Sample const &sample, bool normalize=true)
	Calculate the imbalance of placement mass for each Edge of the given Sample. More...
void	epca_splitify_transform (utils::Matrix< double > &imbalance_matrix, double kappa=1.0)
	Perform a component-wise transformation of the imbalance matrix used for epca(). More...