A toolkit for working with phylogenetic data.
v0.19.0
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epca.hpp File Reference

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Classes

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

Namespaces

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

Functions

EpcaData epca (SampleSet const &samples, double kappa=1.0, double epsilon=1e-5, size_t components=0)
 Perform EdgePCA on a SampleSet. More...
 
std::vector< size_t > epca_filter_constant_columns (utils::Matrix< double > &imbalance_matrix, double epsilon=1e-5)
 Filter out columns that have nearly constant values, measured using an epsilon. 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...