compile_admb: Compile ADMB files, run, read output

In R2admb: 'ADMB' to R Interface Functions

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

R2admb documentation built on Nov. 10, 2022, 5:59 p.m.