run_stocksynthesis: Function to execute an SS run

In r4atlantis/atlantisom: Generates Data Sets From Atlantis Scenarios

Function to execute an SS run

Description

This function runs stock synthesis in the specified directory for the model name given. It is copied almost verbatim from ss3sim::run_ss3model().

Usage

run_stocksynthesis(
  os,
  species,
  model_dir,
  admb_options = " -noest",
  ignore.stdout = TRUE,
  show_output = FALSE,
  iteration_pause = 0.05,
  ...
)

Arguments

species	species name
model_dir	directory containing the model files
admb_options	options for running admb, like "-nohess", "-noest"
ignore.stdout	Logical: passed on to system.
show_output	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.
iteration_pause	how long to pause between model iterations if this function is called in a loop
...	Anything else to pass to system
ss_name	name of the ss model contained within

r4atlantis/atlantisom documentation built on Nov. 12, 2023, 2:59 a.m.