A toolkit for working with phylogenetic data.
v0.20.0
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masses.cpp File Reference

Detailed Description

Implementation of the Placement Functions.

Definition in file masses.cpp.

#include "genesis/placement/function/masses.hpp"
#include "genesis/placement/function/helper.hpp"
#include "genesis/placement/function/operators.hpp"
#include "genesis/tree/default/distances.hpp"
#include "genesis/tree/default/functions.hpp"
#include "genesis/tree/function/distances.hpp"
#include "genesis/tree/function/functions.hpp"
#include "genesis/tree/function/operators.hpp"
#include "genesis/utils/core/algorithm.hpp"
#include "genesis/utils/core/std.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <exception>
#include <regex>
#include <string>
#include <unordered_map>
#include <unordered_set>
#include <vector>

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

std::vector< double > placement_mass_per_edge_without_multiplicities (Sample const &sample)
 Return a vector that contains the sum of the masses of the PqueryPlacements per edge of the tree of the Sample. More...
 
utils::Matrix< double > placement_mass_per_edge_without_multiplicities (SampleSet const &sample_set)
 Return a Matrix that contains the placement masses per edge. More...
 
std::vector< double > placement_mass_per_edges_with_multiplicities (Sample const &sample)
 Return a vector that contains the sum of the masses of the PqueryPlacements per edge of the tree of the Sample, using the multiplicities as factors. More...
 
utils::Matrix< double > placement_mass_per_edges_with_multiplicities (SampleSet const &sample_set)
 Return a Matrix that contains the placement masses per edge, using the multiplicities as factors. More...
 
double total_multiplicity (Pquery const &pqry)
 Return the sum of all multiplicities of the Pquery. More...
 
double total_multiplicity (Sample const &sample)
 Return the sum of all multiplicities of all the Pqueries of the Sample. More...
 
double total_placement_mass_with_multiplicities (Sample const &smp)
 Get the mass of all PqueryPlacements of the Sample, using the multiplicities as factors. More...
 
double total_placement_mass_without_multiplicities (Sample const &smp)
 Get the summed mass of all PqueryPlacements in all Pqueries of the given Sample, where mass is measured by the like_weight_ratios of the PqueryPlacements. More...