ObtainigValueSPBal: Obtaining the selected principal balances values

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Obtaining the selected principal balances values

Description

Calculates the value of the selected principal balances (SPBal) of the BPBM model at all time points.

Usage

ObtainigValueSPBal(Num, Dem, especie, Tt)

Arguments

Num	List. The component i of the list has the number of the row of the matrix especie where the bacteria in the numerator of the principal balance i are placed.
Dem	List. The component i of the list has the number of the row of the matrix especie where the bacteria in the denominator of the principal balance i are placed.
especie	Matrix that contains at row i the bacterial taxa of bacteria i at all time points.
Tt	Number of time points available

Value

Returns a list with:

• NumSPBal: List. The component i of the list has the number of the row of the matrix especie where the bacteria in the numerator of the selected principal balance i are placed.

• DemSPBal: List. The component i of the list has the number of the row of the matrix especie where the bacteria in the denominator of the selected principal balance i are placed.

• MatrixSPBal: MatrixSPBal is the matrix that contains the covariates of the model. The first line es equal to 1 for all columns. The other rows contain the value of one SPBal at all time points. The selected principal balance of the row i+1 has at its numerator the bacteria placed in the rows NumSPBal[[i]] of the "especie". The selected principal balance of the row i+1 has at its denominator the bacteria placed in the rows DemSPBal[[i]] of the "especie".

• PercenVarianceSPBal: Vector. The component of the vector i contains the percentage of variance of the SPBal with numerator NumSPBal[[i]] and denominator DemSPBal[[i]].

References

Creus-Martí, I., Moya, A., Santonja, F. J. (2022). Bayesian hierarchical compositional models for analysing longitudinal abundance data from microbiome studies. Complexity, 2022.

Examples

set.seed(314)
esp2=t(gtools::rdirichlet(n=6, c(1,1,5,1,1)))

Num2<-list(3,c(3,5),1,c(3,5,4))
Dem2<-list(5,4,2,c(1,2))

ObtainigValueSPBal(Num2,Dem2,esp2,6)

CoDaLoMic documentation built on April 12, 2025, 2:18 a.m.