R: Run an Executable Binary File in MCMC Mode

runMC {PBSadmb}

R Documentation

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, Pacific Biological Station, Nanaimo BC, Canada