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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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#include <genesis/tree/mass_tree/balances.hpp>
Data needed to calculate balances.
This data is needed for calculations such as mass_balance(), phylogenetic_ilr_transform(), and phylogenetic_factorization(). Use mass_balance_data( std::vector<MassTree> const&, ... ) to calculate this data, and see BalanceSettings for the settings to tune these calculations.
Definition at line 170 of file balances.hpp.
Public Attributes | |
| utils::Matrix< double > | edge_masses |
| The relative per-edge masses per original input Tree. More... | |
| utils::Matrix< double > | raw_edge_masses |
| The absolute raw per-edge masses per original input Tree. More... | |
| std::vector< double > | taxon_weights |
| The taxon/edge weights calculated from mulitple trees. More... | |
| Tree | tree |
| The Tree on which to calculate balances. More... | |
| utils::Matrix<double> edge_masses |
The relative per-edge masses per original input Tree.
Each row corresponds to a Tree/Sample, each column to the edges of the trees, stored in the order of their indices.
The masses are relative, that is, they were divided by their sum per row. Furthermore, prior to this normalization, pseudeo-counts might be added to the masses in order to compensate for zero values (which are not valid in balance calculations). Also, if taxon weighing is used, the masses are divided by their weight. See BalanceSettings for the possible options for pseudo-counts. These are the values that are used for the balances computations.
In order to get the absolute masses without taxon weighing, and without normalization, see raw_edge_masses.
Definition at line 197 of file balances.hpp.
| utils::Matrix<double> raw_edge_masses |
The absolute raw per-edge masses per original input Tree.
Each row corresponds to a Tree/Sample, each column to the edges of the trees, stored in the order of their indices.
The masses are absolute, that is, they just add up the MassTreeEdgeData::masses per edge. Furthermore, pseudeo-counts might be added to the masses in order to compensate for zero values (which are not valid in balance calculations). See BalanceSettings for the possible options for pseudo-counts.
In order to get the final edge masses that are used in the balances computation, see edge_masses.
Definition at line 213 of file balances.hpp.
| std::vector<double> taxon_weights |
The taxon/edge weights calculated from mulitple trees.
These weights are used in soft thresholding as described in Section "Soft thresholding through weighting taxa" of [1]. See there for details. See BalanceSettings for the possible options to calculate these weights. The weights are calculated per edge of the tree, which we call taxa here, to avoid confusion of masses and weights.
[1] J. D. Silverman, A. D. Washburne, S. Mukherjee, and L. A. David, "A phylogenetic transform enhances analysis of compositional microbiota data," Elife, vol. 6, p. e21887, Feb. 2017. https://elifesciences.org/articles/21887
Definition at line 229 of file balances.hpp.
| Tree tree |
The Tree on which to calculate balances.
As multiple input tress need to have the same topology, it suffices to store just one copy. This copy is not a MassTree any more, in order to avoid accidents of trying to re-use this tree for mass calculations. Instead, it is a simple CommonTree.
Definition at line 179 of file balances.hpp.
1.8.17