Estimate_Param_EstParmFunc {CoDaLoMic}R Documentation

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:

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)



[Package CoDaLoMic version 0.1.1 Index]