#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...  

strong 
Enumerator  

kNone  Use no norm, that is, use 
kManhattan  Use the Manhattan norm of the relative abundances of the taxon.

kEuclidean  Use the Euclidean norm of the relative abundances of the taxon.

kMaximum  Use the Maximum norm of the relative abundances of the taxon.

kAitchison  Use the Aitchison norm of the relative abundances of the taxon.

Definition at line 104 of file balances.hpp.

strong 
Enumerator  

kNone  Use no tendency, that is, use 
kMedian  Use the median of the taxon masses.

kArithmeticMean  Use the arithmetic mean of the taxon masses.

kGeometricMean  Use the geometric mean of the taxon masses.

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.