runMC {PBSadmb}

Run an Executable Binary File in MCMC Mode

Description

Run the executable binary file 'prefix'.exe, created by makeAD, to generate MCMC simulations.

Usage

runMC(prefix, nsims=2000, nthin=20, outsuff=".mc.dat",
      logfile=FALSE, add=TRUE, verbose=TRUE)

Arguments

prefix

string name prefix of the ADMB project (e.g., "vonb").

nsims

numeric scalar indicating number of MCMC simulations to perform.

nthin

numeric scalar indicating the sampling rate or thinning of the nsims MCMC simulations to report.

outsuff

string name suffix of the MCMC output data file.

logfile

logical: if TRUE, create a log file of the messages from the shell call.

add

logical: if TRUE, append shell call messages to an exsiting log file.

verbose

logical: if TRUE, report the shell call an its messages to the R console.

Details

This function runs 'prefix'.exe twice, first with the arguments -mcmc 'nsims' -mcsave 'nthin' and second with the argument -mceval. By default, output goes to the file 'prefix'.mc.dat, although a user can specify a different output suffix.

To see this function in action, use the PBSadmb GUI with the example vonb or simpleMC.

Value

Invisibly returns the results of the shell call.

Note

A wrapper function that can be called from a GUI exists as .win.runMC.

Author(s)

Jon T. Schnute, Scientist Emeritus
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
Last modified Rd: 2009-09-10

See Also

runAD, makeAD, cleanAD