ARZIMM.control: internal ARZIMM parameters

In Hlch1992/Rprojects: Statistical modeling and inference of microbial interaction and stability for microbial dynamical systems

Description

View and/or change the factory default parameters in ARZIMM

Usage

ARZIMM.control(
  initpara = list(betaini = NULL, gammaini = NULL, sigmaini = NULL, weight1all = NULL,
    weight2all = NULL, calini = TRUE, iniw = FALSE),
  tunpara = list(lambdaseq1 = NULL, lambdaseq2 = NULL, ntun = 50, epsilon = c(50000, 5)),
  selectpara = list(selgamma = TRUE, selcri = "BIC", pen = "adalasso"),
  bootpara = list(bootpval = TRUE, nboot = 500)
)

Arguments

initpara	a named list of user-specified initial values: betaini the matrix of fixed effects for the non-zero auto-regressive model gammaini the matrix of fixed effects for the zero state logit model sigmaini the measurement error standard deviation for both the non-zero auto-regressive model and the zero state logit model weight1all observation weights for the non-zero auto-regressive model. Default is 1 for each observation weight2all observation weights for the zero state logit model. Default is 1 for each observation calini=T logical; should initial parameters be calculated. Default is Ture iniw logical; should observation weights be calculated according to initial parameters. Default is False When this list of initial values does not contain some of these components or contains components not of the appropriate length, then the default initial values are used instead.
tunpara	a list of control values with components: lambdaseq1 a user supplied lambda sequence for the non-zero auto-regressive model. Typical usage is to have the program compute its own lambda sequence. Supplying a value of lambda overrides this. WARNING: use with care. Avoid supplying a single value for lambda lambdaseq2 a user supplied lambda sequence for the zero state logit model. Typical usage is to have the program compute its own lambda sequence. Supplying a value of lambda overrides this. WARNING: use with care. Avoid supplying a single value for lambda ntun the number of lambda values - default is 50 epsilon the range of lambda values; default= c(5e4,5)
selectpara	a list of control values with components: selgamma logical; should concomitant variables in the zero state logit model be selected selcri method to be use for variable selection. Currently three options. The default is BIC. Other choices are AIC and CV pen penalty; defualt is 'adalasso'
bootpara	a list of control values with components: bootpval logical; should p value be calculated using bootstrap nboot the number of bootstrap simulations; default is 500

Details

If called with no arguments, ARZIMM.control() returns a list with the current settings of these parameters. Any arguments included in the call sets those parameters to the new values, and then silently returns. The values set are persistent for the duration of the R session.

Value

A list with named elements as in the argument list

Author(s)

Linchen He
Maintainer: Linchen He [e-mail]

See Also

ARZIMM

Examples

ARZIMM.control(bootpara=list(bootpval=FALSE))
ARZIMM.control(selectpara=list(selgamma=FALSE,pen='lasso'))

Hlch1992/Rprojects documentation built on Feb. 10, 2020, 12:30 a.m.