ObtainigValueSPBal {CoDaLoMic} | R Documentation |
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 |
Dem |
List. The component i of the list has the number of the row of the matrix |
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 rowsDemSPBal[[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 denominatorDemSPBal[[i]]
.
References
Creus-MartÃ, 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)