compile_admb: Compile ADMB files, run, read output

In R2admb: ADMB to R interface functions

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,
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?
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)
verbose	(logical) Verbose output?
admb_errors	(character) how to handle compilation/linking errors?
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 May 2, 2019, 5:19 p.m.