run_ss3model: Run an operating or estimation model for a specified set of...
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description Usage Arguments Details Author(s) See Also

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.

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

`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`.

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 #'

Sean C. Anderson

ss3sim_base, run_ss3sim

ss3sim documentation built on Nov. 9, 2019, 1:06 a.m.