A toolkit for working with phylogenetic data.
v0.18.0
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measures.hpp File Reference

Detailed Description

Header for Placement Measures functions.

Definition in file measures.hpp.

#include "genesis/placement/placement_tree.hpp"
#include <cstddef>
#include <utility>
#include <vector>

Go to the source code of this file.

Classes

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::utils
 

Functions

double edpl (Sample const &sample, Pquery const &pquery)
 Shortcut alias for expected_distance_between_placement_locations(). More...
 
std::vector< double > edpl (Sample const &sample)
 Shortcut alias for expected_distance_between_placement_locations(). More...
 
double expected_distance_between_placement_locations (Pquery const &pquery, utils::Matrix< double > const &node_distances)
 Calculate the EDPL uncertainty values for a Pquery. More...
 
double expected_distance_between_placement_locations (Sample const &sample, Pquery const &pquery)
 Calculate the EDPL uncertainty values for a Pquery. More...
 
std::vector< double > expected_distance_between_placement_locations (Sample const &sample)
 Calculate the expected_distance_between_placement_locations() for all Pqueries in the Sample. More...
 
double pairwise_distance (const Sample &smp_a, const Sample &smp_b, bool with_pendant_length=false)
 Calculate the normalized pairwise distance between all placements of the two Samples. More...
 
double placement_distance (PqueryPlacement const &place_a, PqueryPlacement const &place_b, utils::Matrix< double > const &node_distances)
 
double pquery_distance (const PqueryPlain &pqry_a, const PqueryPlain &pqry_b, const utils::Matrix< double > &node_distances, bool with_pendant_length=false)
 Calculates the normalized distance between two plain pqueries. It is mainly a helper method for distance calculations (e.g., pairwise distance, variance). More...
 
double variance (const Sample &smp, bool with_pendant_length=false)
 Calculate the variance of the placements on a tree. More...