A toolkit for working with phylogenetic data.
v0.24.0
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

static void fill_node_distance_histogram_set_ (Sample const &sample, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, NodeDistanceHistogramSet &histogram_set)
 Local helper function to fill the placements of a Sample into Histograms. More...
 
static NodeDistanceHistogramSet make_empty_node_distance_histogram_set_ (tree::Tree const &tree, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, size_t const histogram_bins)
 Local helper function to create a set of Histograms without any weights for a given Tree. More...
 
NodeDistanceHistogramSet node_distance_histogram_set (Sample const &sample, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, size_t const histogram_bins)
 Calculate the NodeDistanceHistogramSet representing a single Sample, given the necessary matrices of this Sample. More...
 
static NodeDistanceHistogramSet node_distance_histogram_set (Sample const &sample, size_t const histogram_bins)
 
static std::vector< NodeDistanceHistogramSet > node_distance_histogram_set (SampleSet const &sample_set, size_t const histogram_bins)
 Local helper function that calculates all Histograms for all Samples in a SampleSet. More...
 
static double node_histogram_distance (NodeDistanceHistogram const &lhs, NodeDistanceHistogram const &rhs)
 
double node_histogram_distance (NodeDistanceHistogramSet const &lhs, NodeDistanceHistogramSet const &rhs)
 Given the histogram sets that describe two Samples, calculate their distance. More...
 
utils::Matrix< double > node_histogram_distance (std::vector< NodeDistanceHistogramSet > const &histogram_sets)
 Given the histogram sets that describe a set of Samples, calculate their pairwise distance matrix. More...
 
double node_histogram_distance (Sample const &sample_a, Sample const &sample_b, size_t const histogram_bins=25)
 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)
 Calculate the Node Histogram Distance of every pair of Samples in the SampleSet. More...