phylo_factor.hpp File Reference

#include "genesis/tree/mass_tree/balances.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include <functional>
#include <unordered_set>
#include <vector>

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Classes
struct	PhyloFactor
	A single phylogenetic factor. More...

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::tree

Typedefs
using	PhyloFactorObjectiveFunction = std::function< double(size_t iteration, size_t edge_index, std::vector< double > const &balances) >
	Function type used as the objective function in phylogenetic_factorization(). More...

Functions
PhyloFactor	phylo_factor_find_best_edge (size_t iteration, BalanceData const &data, std::unordered_set< size_t > const &candidate_edges, PhyloFactorObjectiveFunction objective)
	Helper function for phylogenetic_factorization() that tries all candidate edges to find the one that maximizes the objective function. More...
std::unordered_set< size_t >	phylo_factor_subtree_indices (Subtree const &subtree, std::unordered_set< size_t > const &candidate_edges)
	Helper function for phylogenetic_factorization() to find the constrained subtrees that are split by an edge. More...
std::vector< PhyloFactor >	phylogenetic_factorization (BalanceData const &data, PhyloFactorObjectiveFunction objective, size_t max_iterations=0, std::function< void(size_t iteration, size_t max_iterations)> log_progress={})
	Calculate the Phylogenetic Factorization (PhyloFactor) of a set of MassTrees. More...
std::vector< PhyloFactor >	phylogenetic_factorization (BalanceData const &data, std::function< double(std::vector< double > const &balances)> objective, size_t max_iterations=0, std::function< void(size_t iteration, size_t max_iterations)> log_progress={})
	Calculate the Phylogenetic Factorization (PhyloFactor) of a set of MassTrees. More...