Fisheries stock assessment simulation testing with Stock Synthesis


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Documentation for package ‘ss3sim’ version 0.8.2

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ss3sim-package ss3sim: Fisheries stock assessment simulation testing with Stock Synthesis
bias_ss3 Perform a single bias adjustment run
calculate_runtime Calculate run time
change_agecomp Sample age compositions from expected values
change_e Methods to alter which parameters are estimated in a SS3 '.ctl' file.
change_f Alter the fishing mortality (F) values in an 'ss3.par' file
change_index Sample the biomass with observation error
change_lcomp Sample length compositions from expected values
change_rec_devs Replace recruitment deviations
change_retro Alter a starter file for a retrospective analysis
change_tv Methods to include time-varying parameters in an SS3 operating model
cleanup_ss3 Clean up after an SS3 run
copy_ss3models Copy the operating and estimation models and create a folder structure
create_argfiles Create template argument input files
expand_scenarios Create vectors of scenario IDs
extract_expected_data Extract the expected data values
get_args Take a csv file, read it, and turn the first column into the list names and the second column into the list values.
get_caseargs Take a scenario ID and return argument lists
get_caseval Take a scenario ID and a case type and return the case number
get_fish600_casefolder Get the folder location of the FISH600 case files
get_model_folder Get the folder location of an included SS3 model configuration
get_recdevs Return a set of recruitment deviations
get_results_all Extract SS3 simulation output
get_results_scalar Extract scalar quantities from a model run.
get_results_scenario Extract SS3 simulation results for one scenario.
get_results_timeseries Extract time series from a model run.
get_sigmar Get recruitment deviation sigma
is_f Check if a string is a function
pastef Paste with "/" as the separator
run_bias_ss3 Determine level of bias adjustment for SS3 runs
run_ss3model Run an operating or estimation model for a specified set of scenario IDs
run_ss3sim Master function to run SS3 simulations
sanitize_admb_options Check admb options to make sure there aren't flags there shouldn't be
scalar_dat Example scalar data from the ss3sim vignette
setup_parallel Setup parallel processing
ss3sim ss3sim: Fisheries stock assessment simulation testing with Stock Synthesis
ss3sim_base Base wrapper fun to run an ss3sim simulation
substr_r Substring from right
ts_dat Example time series data from the ss3sim vignette
verify_input Verify and standardize SS3 input files