#include <genesis/tree/mass_tree/balances.hpp>
Settings to calculate balances and the Phylogenetic ILR Transform.
The class stores settings for different parts of the balances calculation:
p
as described there, offering different ways to assess the central tendency of counts and to measure the norm of their relative abundances. These two terms (BalanceSettings::tendency and BalanceSettings::norm) are multiplied to get the weight for a taxon. By default, the geometric mean times the euclidean norm are used as 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 76 of file balances.hpp.
Public Types | |
enum | WeightNorm { kNone, kManhattan, kEuclidean, kMaximum, kAitchison } |
enum | WeightTendency { kNone, kMedian, kArithmeticMean, kGeometricMean } |
Public Attributes | |
WeightNorm | norm = WeightNorm::kEuclidean |
Set the term for the norm of relative abundances for calculating the taxon weights. More... | |
double | pseudo_count_summand_all = 1.0 |
Set the constant that is added to all taxon masses to avoid zero counts. More... | |
double | pseudo_count_summand_zeros = 0.0 |
Set the constant that is added to taxon masses that are zero, to avoid zero counts. More... | |
WeightTendency | tendency = WeightTendency::kGeometricMean |
Set the term for asssing the central tendency of taxon masses for calculating the taxon weights. More... | |
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strong |
Enumerator | |
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kNone | Use no norm, that is, use |
kManhattan | Use the Manhattan norm of the relative abundances of the taxon.
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kEuclidean | Use the Euclidean norm of the relative abundances of the taxon.
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kMaximum | Use the Maximum norm of the relative abundances of the taxon.
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kAitchison | Use the Aitchison norm of the relative abundances of the taxon.
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Definition at line 104 of file balances.hpp.
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strong |
Enumerator | |
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kNone | Use no tendency, that is, use |
kMedian | Use the median of the taxon masses.
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kArithmeticMean | Use the arithmetic mean of the taxon masses.
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kGeometricMean | Use the geometric mean of the taxon masses.
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Definition at line 78 of file balances.hpp.
WeightNorm norm = WeightNorm::kEuclidean |
Set the term for the norm of relative abundances for calculating the taxon weights.
Definition at line 145 of file balances.hpp.
double pseudo_count_summand_all = 1.0 |
Set the constant that is added to all taxon masses to avoid zero counts.
Definition at line 150 of file balances.hpp.
double pseudo_count_summand_zeros = 0.0 |
Set the constant that is added to taxon masses that are zero, to avoid zero counts.
Definition at line 155 of file balances.hpp.
WeightTendency tendency = WeightTendency::kGeometricMean |
Set the term for asssing the central tendency of taxon masses for calculating the taxon weights.
Definition at line 140 of file balances.hpp.