compile_admb {R2admb}

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

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

• compile_admb returns nothing (it has the side effect of creating an executable)

• run_admb invisibly returns the output produced by the ADMB run; it also produces output files on disk as a side effect

• read_admb returns an object of class admb, containing as much information as possible gleaned from the output files (parameter estimates, standard errors, variance-covariance matrix, profiles, MCMC output)

Note

Compiling also sets executable mode.

Author(s)

Ben Bolker