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 |