compile_admb: Compile ADMB files, run, read output

Description

With various tests, calls the admb script to compile from a TPL file to an executable, or runs the resulting executable

Usage

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compile_admb(fn,safe=FALSE,re=FALSE,
verbose=FALSE,
admb_errors=c("stop","warn","ignore"))

 run_admb(fn,verbose=FALSE,mcmc=FALSE,
mcmc.opts=mcmc.control(),profile=FALSE,
extra.args="",admb_errors=c("stop","warn","ignore"))

read_admb(fn,verbose=FALSE,profile=FALSE,
mcmc=FALSE,mcmc.opts=NULL,admbOut=NULL,checkterm=TRUE)

Arguments

fn

(character) name of TPL file, without extension

safe

(logical) Compile in safe mode?

re

(logical) Compile in random effects (ADMB-RE) mode?

verbose

(logical) Verbose output?

admb_errors

(character) how to handle compilation/linking errors?

profile

(logical) Run likelihood profiles?

extra.args

(character) extra arguments for ADMB run

mcmc

(logical) run post-hoc MCMC?

mcmc.opts

options for MCMC run (see mcmc.control)

admbOut

(character) ADMB run output for inclusion in admb object (for internal use)

checkterm

(logical) compute termination criteria (ratio of min/max eigenvalue) and include it in the saved object?

Value

Note

Compiling also sets executable mode.

Author(s)

Ben Bolker


Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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