A toolkit for working with phylogenetic data.
v0.19.0
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
nhd.cpp File Reference

Go to the source code of this file.

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_histogram_set (Sample const &sample, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, NodeDistanceHistogramSet &histogram_set)
 Fill the placements of a Sample into Histograms. More...
 
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)
 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)
 Calcualte the NodeDistanceHistogramSet representing a single Sample, given the necessary matrices of this Sample. More...
 
NodeDistanceHistogramSet node_distance_histogram_set (Sample const &sample, size_t const histogram_bins)
 
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...
 
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...