runMC {PBSadmb} | R Documentation |
Run the executable binary file 'prefix'.exe
, created by
makeAD
, to generate MCMC simulations.
runMC(prefix, nsims=2000, nthin=20, outsuff=".mc.dat", logfile=FALSE, add=TRUE, verbose=TRUE)
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. |
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
.
Invisibly returns the results of the shell call.
A wrapper function that can be called from a GUI exists as .win.runMC
.
Jon T. Schnute, Pacific Biological Station, Nanaimo BC, Canada