run_ss3model {ss3sim}

Run an operating or estimation model for a specified set of scenario IDs

Description

This function takes care of calling SS3. Importantly, it parses whether the user is on Unix or Windows and calls the binary correctly. This lower-level function is meant to be called by higher level functions such as run_ss3sim, ss3sim_base, or your own custom function.

Usage

run_ss3model(scenarios, iterations, type = c("om", "em"),
  admb_options = "", hess = FALSE, ignore.stdout = TRUE,
  admb_pause = 0.05, show.output.on.console = FALSE, ...)

Arguments

scenarios

Which scenarios to run. Controls which folder contains the model that SS3 should run on.

iterations

Which iterations to run. Controls which folder contains the model that SS3 should run on.

type

Are you running the operating or estimation models?

admb_options

Any additional options to pass to the SS3 command.

hess

Calculate the Hessian on estimation model runs?

ignore.stdout

Passed to system. If TRUE then ADMB output is not printed on screen. This will be slightly faster. Set to FALSE to help with debugging.

admb_pause

A length of time (in seconds) to pause after running the simulation model. This can be necessary on certain computers where file writing can be slightly delayed. For example, on computers where the files are written over a network connection. If the output files haven't finished writing before R starts looking for the output then the simulation will crash with an error about missing files. The default value is set to 0.01 seconds, just to be safe.

show.output.on.console

Logical: passed on to system.

...

Anything else to pass to system.

Details

ss3sim requires you to place the SS executable in your path. See the vignette vignette("ss3sim-vignette") for details on this process. The executables themselves can be downloaded from: https://www.dropbox.com/sh/zg0sec6j20sfyyz/AACQiuk787qW882U2euVKoPna #'

Author(s)

Sean C. Anderson

See Also

ss3sim_base, run_ss3sim