A toolkit for working with phylogenetic data.
v0.18.0
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nhd.cpp File Reference

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Namespaces

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

Functions

void fill_node_distance_histograms (Sample const &sample, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, std::vector< utils::Histogram > &histograms)
 Fill the placements of a Sample into Histograms. More...
 
std::vector< utils::Histogram > make_empty_node_distance_histograms (tree::Tree const &tree, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, size_t const histogram_bins)
 Create a set of Histograms without any weights for a given Tree. More...
 
std::vector< utils::Histogram > node_distance_histograms (Sample const &sample, size_t const histogram_bins, bool use_negative_axis=true)
 Local helper function that calculates the Histograms for a Sample. More...
 
std::vector< std::vector
< utils::Histogram > > 
node_distance_histograms (SampleSet const &sample_set, size_t const histogram_bins, bool use_negative_axis=true)
 Local helper function that calculates all Histograms for all Samples in a SampleSet. More...
 
std::vector< utils::Histogram > node_distance_histograms_old (Sample const &sample, size_t const histogram_bins)
 Local helper function to calculate the histograms of distances from all Nodes of the Tree of a Sample to all its PqueryPlacements. More...
 
double node_histogram_distance (Sample const &sample_a, Sample const &sample_b, size_t const histogram_bins=25, bool use_negative_axis=true)
 Calculate the Node Histogram Distance of two Samples. More...
 
utils::Matrix< double > node_histogram_distance (SampleSet const &sample_set, size_t const histogram_bins=25, bool use_negative_axis=true)
 Calculate the node_histogram_distance() for every pair of Samples in the SampleSet. More...
 
double node_histogram_distance_old (Sample const &sample_a, Sample const &sample_b, size_t const histogram_bins)
 
utils::Matrix< double > node_histogram_distance_old (SampleSet const &sample_set, size_t const histogram_bins)
 
double node_histogram_emd (std::vector< utils::Histogram > const &lhs, std::vector< utils::Histogram > const &rhs, size_t const node_count)
 Local helper function to calculate the sum of histogram emds between two sets of histograms. More...