A toolkit for working with phylogenetic data.
v0.24.0
PhyloFactor Struct Reference

#include <genesis/tree/mass_tree/phylo_factor.hpp>

Detailed Description

A single phylogenetic factor.

See also
phylogenetic_factorization()

Definition at line 61 of file phylo_factor.hpp.

Public Attributes

std::vector< double > all_objective_values
 For reference, all other objective values for the other edges of the tree. More...
 
std::vector< double > balances
 The balances for all Samples calculated on the two sets of edge indices of this factor. More...
 
size_t edge_index
 The edge that this factor found to be maximizing for the objective function. More...
 
std::unordered_set< size_t > edge_indices_primary
 The set of edges on the root (primary) side of the edge that belongs to this factor. More...
 
std::unordered_set< size_t > edge_indices_secondary
 The set of edges on the non-root (secondary) side of the edge that belongs to this factor. More...
 
double objective_value
 The objective value obtained from the objective function using the balances. More...
 

Member Data Documentation

◆ all_objective_values

std::vector<double> all_objective_values

For reference, all other objective values for the other edges of the tree.

This is mainly used for visualization purposes in order to validate why a particular edge has been chosen as the next factor. This shows the objective value for all edges that have not yet been factored out by previous iterations.

The vector is indexed by edge indices as usual. The edges of previous factors as well as leaf edges have a NaN value to distinguish them from proper values.

Definition at line 98 of file phylo_factor.hpp.

◆ balances

std::vector<double> balances

The balances for all Samples calculated on the two sets of edge indices of this factor.

Definition at line 81 of file phylo_factor.hpp.

◆ edge_index

size_t edge_index

The edge that this factor found to be maximizing for the objective function.

Definition at line 66 of file phylo_factor.hpp.

◆ edge_indices_primary

std::unordered_set<size_t> edge_indices_primary

The set of edges on the root (primary) side of the edge that belongs to this factor.

Definition at line 71 of file phylo_factor.hpp.

◆ edge_indices_secondary

std::unordered_set<size_t> edge_indices_secondary

The set of edges on the non-root (secondary) side of the edge that belongs to this factor.

Definition at line 76 of file phylo_factor.hpp.

◆ objective_value

double objective_value

The objective value obtained from the objective function using the balances.

Definition at line 86 of file phylo_factor.hpp.


The documentation for this struct was generated from the following file: