FromVectorToMatrix_BPBM: Writting the parameters in the matrix form required in BPBM...

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Writting the parameters in the matrix form required in BPBM model

Description

StudyingParam returns a matrix where the value of the parameters is in the column "mean". This function inputs this columns and outputs the parameters in the matrix form required by the BPBM model.

Usage

FromVectorToMatrix_BPBM(param, MatrizPBmodelo, E)

Arguments

param	Vector. Column "mean" of the output of "StudyingParam" function.
MatrizPBmodelo	Matrix with the covariates of the model. In an example with two SPBal and three time points, the covariates are written in the following order: 1 1 1 SPBal_{1,t-1} SPBal_{1,t-2} SPBal_{1,t-3} SPBal_{2,t-1} SPBal_{2,t-2} SPBal_{2,t-3}
E	Number of bacteria in the dataset.

Value

Returns a matrix with the parameters in the order required by the BPBM model.

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)
especie=t(gtools::rdirichlet(n=6, c(6,6,1,6,6)))
E=5
Tt=6
MatrizPBmodelo=rbind(c(1,1,1,1,1,1),
                   c(-0.3,0.4,0.3,-0.7,-0.4,-0.6),
                   c(0.3,0.5,-0.3,0.1,0.4,0.1))

est=Estimating_BPBM(especie,
                   Tt,
                   E,
                   MatrizPBmodelo,
                   nn.chain=3,
                   nn.burnin=1000,
                   nn.sample=5000,
                   nn.thin=10)

mm=StudyingParam(est$R2jagsOutput$BUGSoutput$summary,est$SamplesAllChains)
FromVectorToMatrix_BPBM(mm$Param.Summary[,"mean"],MatrizPBmodelo,5)

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