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
