A library for working with phylogenetic and population genetic data.
epca.hpp File Reference

Go to the source code of this file.


struct  EpcaData
 Helper stucture that collects the output of epca(). More...


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


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...