EstParmFunc_FBM: Writting the loglikelihood of the dirichlet

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Writting the loglikelihood of the dirichlet

Description

This function calculates the loglikelihood of the dirichlet for the FBM model.

Usage

EstParmFunc_FBM(param, especie, E, EspecieMaxima, Tt, especiemodi)

Arguments

param	Vector with the parameters in the following order: a11,a12,a13, a21, a22,a23, ...a(D-1)1,a(D-1)2,a(D-1)3,tau. Where D is the number of bacterial species present in the matrix especie.
especie	Matrix that contains at row i the bacterial taxa of bacteria i at all time points.
E	Number of bacteria available
EspecieMaxima	Row in which the bacterial with maximum mean abundance is in especie.This bacteria is used as reference in the alr transformation that the model does and it is placed at the denominator of the balance)
Tt	Number of bacteria available
especiemodi	Matrix that contains at row i the bacterial taxa of bacteria i at time points t=2,...,Tt. The bacteria are placed in the same order than in especie.

Details

The regression of this model is defined by

\mu_{it}=a_{i1}+a_{i2}\cdot\text{alr}(x_{i,(t-1)})+a_{i3}\cdot\text{Balance}(x_{i,(t-1)})\text{ for }i=1,\dots, D-1\text{ where } D \text{ is the number of bacteria}

Value

Returns a number with the value of the dirichlet loglikelihood.

References

Creus-Martí, I., Moya, A., Santonja, F. J. (2021). A Dirichlet autoregressive model for the analysis of microbiota time-series data. Complexity, 2021, 1-16.

Examples

especie1=cbind(c(0.5,0.3,0.2), c(0.1,0.3,0.6))
especiemodi=especie1[,-1]
tau1=0.4
parms1= cbind(c(0.1,0.2),c(-0.2,0.1),c(0.3,0.2))
parms11=c(as.vector( t(parms1)),tau1)

EstParmFunc_FBM(parms11,especie1,3 ,3  , 2,especiemodi)

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