Run MCMC using adnuts for SS3
run_mcmc_diagnostics(
dir_wd,
model = "ss3",
extension = ".exe",
iter = 2000,
chains = 2,
hour = 1,
interactive = FALSE,
verbose = FALSE
)A file path to the directory where the model files and the executable are saved. This can be relative to your current working directory or a full path. Your working directory will be changed while executing the function to be inside the location provided in this argument but upon exiting it will return to your current working directory.
A string giving the name of the executable without an
an extension. The extension is provided in extension. Do not include
any path information, just the name of the executable. For example, the
default is "ss3".
A string giving the extension for the executable name
provided in model. The default is .exe, which works on Windows
machines.
A numeric value for the number of MCMC draws to do. Default is 2000.
A numeric value for the number of chains to run. Default is 2.
A numeric value that controls the thin rate. The thin rate is calculated based upon the length of time to run the model to allow the function to run in a pre-specified amount of time. For some models, one may want to run this function for longer allowing a greater thin rate. The default is 1 hour.
A logical, where TRUE will run
adnuts::launch_shinyadmb(). The default is FALSE.
A logical, specifying if information should be printed
to the screen. The default is FALSE but using TRUE can be helpful
when you are first running the function or when you have a very unstable
model.