PhyloFactor Struct Reference

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

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... | |

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.

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.

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.

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.

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.

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: