Estimate_Param_EstParmFunc: Estimating Parameters of EstParmFunc

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Estimating Parameters of EstParmFunc

Description

This function calculates the estimated parameters of the Dirich-gLV model.

Usage

Estimate_Param_EstParmFunc(Iter.EstParmFunc, paramini, especie, seed = NULL)

Arguments

Iter.EstParmFunc	Number. Number of iterations.
paramini	Initial values of the parameters. Vector equal to c(tau.ini, as.vector(pam.ini)) where:
especie	Matrix that contains at row i the bacterial taxa of bacteria i at all time points. The bacteria placed in the last row of the matrix will be used as reference in the alr transformation.
seed	Number. Set a seed. Default seed=NULL. pam.ini Matrix. Each row has the parameters of each bacteria, following the same structure than pam in EstParmFunc tau.ini Number. Initial value of the tau parameter in the model

Details

Maximum likelihood estimation is used. This function makes an iterative process, it obtains the value of the parameter that maximize the Dirichlet loglikelihood (defined in EstParmFunc) using the Nelder-Mead method and some initial parameters. Then it uses this value as initial parameters and repeats the process Iter.EstParmFunc times.

Value

Returns a list with:

• All.iter: Matrix. Each row has the parameters obtained in each iteration. The parameters are in the columns written in the same order that they are written in paramini. In this matrix we must observe that in the last iterations the values has really similar or equal values, it not, we need to increase the value of Iter.EstParmFunc.

• Param.Estimates: The estimated parameters. The parameters are in the columns written in the same order that they are written in paramini.

References

Creus-Martí, I. and Moya, A. and Santonja, F. J. (2018). A Statistical Model with a Lotka-Volterra Structure for Microbiota Data. Lucas Jodar, Juan Carlos Cortes and Luis Acedo, Modelling for engineering and human behavior 2018, Instituto Universitario de Matematica Multidisciplinar. ISBN: 978-84-09-07541-6

Examples

especie=cbind(c(0.5,0.3,0.2),c(0.1,0.3,0.6))
paramini=c(100,2,3,4,5,6,7)
Estimate_Param_EstParmFunc(5, paramini , especie,714)

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