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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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#include "genesis/tree/mass_tree/functions.hpp"#include "genesis/tree/function/operators.hpp"#include "genesis/tree/iterator/postorder.hpp"#include "genesis/tree/mass_tree/tree.hpp"#include "genesis/tree/tree.hpp"#include "genesis/utils/core/logging.hpp"#include "genesis/utils/containers/matrix.hpp"#include "genesis/utils/containers/matrix/operators.hpp"#include <algorithm>#include <cassert>#include <cmath>#include <stdexcept>#include <utility>#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::tree | |
Functions | |
| double | mass_tree_binify_masses (MassTree &tree, size_t number_of_bins) |
| Accumulate all masses of a MassTree into bins on each branch. More... | |
| double | mass_tree_center_masses_on_branches (MassTree &tree) |
| Accumulate all masses of a MassTree on the centers of their edges. More... | |
| double | mass_tree_center_masses_on_branches_averaged (MassTree &tree) |
| Accumulate all masses of a MassTree at the average mass position per edge. More... | |
| void | mass_tree_clear_masses (MassTree &tree) |
| Clear all masses of a MassTree, while keeping its topology. More... | |
| std::vector< double > | mass_tree_mass_per_edge (MassTree const &tree) |
Return a std::vector that contains the total mass for each edge of the given MassTree. More... | |
| utils::Matrix< double > | mass_tree_mass_per_edge (std::vector< MassTree > const &mass_trees) |
| Return the total mass for each edge of the given MassTrees. More... | |
| std::vector< std::pair< double, double > > | mass_tree_mass_per_edge_averaged (MassTree const &tree) |
Return a std::vector that contains the total Mass for each edge of the given MassTree (second value), as well as the average position of that mass on the branch (in branch lengths units, first value). More... | |
| MassTree | mass_tree_merge_trees (MassTree const &lhs, MassTree const &rhs, double const scaler_lhs=1.0, double const scaler_rhs=1.0) |
| Merge all masses of two MassTrees into one and return it. More... | |
| void | mass_tree_merge_trees_inplace (MassTree &lhs, MassTree const &rhs, double const scaler_lhs=1.0, double const scaler_rhs=1.0) |
| Merge all masses of two MassTrees by adding them to the first MassTree. More... | |
| void | mass_tree_normalize_masses (MassTree &tree) |
Scale all masses of a MassTree so that they sum up to 1.0. More... | |
| void | mass_tree_reverse_signs (MassTree &tree) |
| Reverse the sign of each mass point on a MassTree. More... | |
| void | mass_tree_scale_masses (MassTree &tree, double factor) |
Scale all masses of a MassTree with the multiplicative factor factor. More... | |
| double | mass_tree_sum_of_masses (MassTree const &tree) |
| Return the total sum of all masses on the MassTree. More... | |
| void | mass_tree_transform_to_unit_branch_lengths (MassTree &tree) |
Set all branch lengths of a MassTree to 1.0, while keeping the relative position of all masses on the branches. More... | |
| bool | mass_tree_validate (MassTree const &tree, double valid_total_mass_difference=-1.0) |
| Validate the data on a MassTree. More... | |
| void | mass_trees_make_average_branch_lengths (std::vector< MassTree > &mass_trees) |
| Change the branch lengths of all trees to their average, and move the masses accordingly in a proportional way. More... | |
1.8.17