A toolkit for working with phylogenetic data.
v0.20.0
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nhd.hpp File Reference
#include <cstddef>
#include <vector>

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Classes

struct  NodeDistanceHistogram
 Simple histogram data structure with equal sized bins. More...
 
struct  NodeDistanceHistogramSet
 Collection of NodeDistanceHistograms that describes one Sample. More...
 
class  Matrix< T >
 

Namespaces

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

Functions

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)
 Calcualte the NodeDistanceHistogramSet representing a single Sample, given the necessary matrices of this Sample. More...
 
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...