admbControl: Control options for ADMB

Description Usage Arguments Details Value Troubleshooting Author(s) Examples

Description

Determines options for running AD Model Builder

Usage

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admbControl(impSamp=0,maxfn=500,imaxfn=500,maxph=5,noinit=TRUE,shess=TRUE,
  run=TRUE, ZI_kluge=FALSE, poiss_prob_bound=TRUE)

Arguments

impSamp

Number of importance sampling steps

maxfn

Maximum number of evaluation steps

imaxfn

number of function evaluations used in intermediate optimization steps.

maxph

maximum phase

noinit

Don't initialize random effects before inner optimization: see ADMB-RE reference manual

shess

Use sparse Hessian: see ADMB-RE reference manual

ZI_kluge

retain a zero-inflation term of 0.001 even when zeroInflation=FALSE (for backward compatibility/testing; deprecated)

poiss_prob_bound

add a small term to prevent estimated Poisson probabilities of zero

run

Whether to run ADMB at all. This will write out files to the appropriate working directory, or read existing output files in the working directory (glmmadmb.{std,bar,par,cor}) into a glmmadmb object.

Details

See the AD Model Builder reference manuals at http://admb-project.org/documentation/manuals/admb-user-manuals

Value

Returns a list of options suitable for passing as the admb.opts argument to glmmadmb

Troubleshooting

Some useful tricks for diagnosing and overcoming fitting problems:

Author(s)

Ben Bolker

Examples

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admbControl(impSamp=200)
## Not run: 
## running to produce saved files in directory:
data(bacteria,package="MASS")
bacteria$present <- as.numeric(bacteria$y)-1
## run to generate files
glmmadmb(present ~ trt + I(week > 2), random = ~ 1 | ID,
                     family = "binomial", data = bacteria,
         save.dir="tmp",admb.opts=admbControl(run=FALSE),
         debug=TRUE)
## now run glmmadmb outside of R ...
## ./glmmadmb -maxfn 500 -maxph 5 -noinit -shess
## run to read in data
result <- glmmadmb(present ~ trt + I(week > 2), random = ~ 1 | ID,
                     family = "binomial", data = bacteria,
         save.dir="tmp",admb.opts=admbControl(run=FALSE))

## End(Not run)

bbolker/glmmadmb documentation built on May 11, 2019, 9:29 p.m.