ExpectedValues_EstParmFunc_FBM: Obtainig the value of the dirichlet parameters, the expected...

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Obtainig the value of the dirichlet parameters, the expected value and the variance.

Description

This function calculates the value of the dirichlet parameters, the expected value and the variance for the FBM model.

Usage

ExpectedValues_EstParmFunc_FBM(
  paramEstimadosFinal,
  especie,
  E,
  EspecieMaxima,
  Tt
)

Arguments

paramEstimadosFinal	The estimate 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 bacteria chosen as reference is in especie.This bacteria is used as reference in the alr tranformation that the model does and it is placed at the denominator of the balance).
Tt	Number of time points available.

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 list with:

• Dirichlet.Param: Matrix. Matrix that contains at row i the dirichlet parameter of the bacteria i at all time points.

• Expected.Value: Matrix. Matrix that contains at row i the expected value of the bacteria i at all time points. The bacterias are placed at the same orden than in especies.

• Variance.Value: Matrix. Matrix that contains at row i the variance of the bacteria i at all time points. The bacterias are placed at the same orden than in especies.

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

set.seed(123)
especie=t(gtools::rdirichlet(2,c(1,1,3)))
Tt=2
E=3
tau=5
EspecieMaxima=3
Iter.EstParmFunc=5
parms11=c(0.1,0.2,0.3,0.4,0.5,0.6,tau)

ExpectedValues_EstParmFunc_FBM(parms11 , especie,E,EspecieMaxima,Tt)

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