# Fisheries Stock Assessment Simulation Testing with Stock Synthesis

## Documentation for package ‘ss3sim’ version 1.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ss3sim-package | ss3sim: Fisheries stock assessment simulation testing with Stock Synthesis
add_colnames | Create matching column names across a list of data frames
add_CPUE | Add a q setup line into an SS control file
add_nulls | Add 'NULL' values to non-existent list elements
add_tv_parlines | Add short time varying parameter lines. At time of writing, this method will work for MG, selectivity, and catchability time varying, but not for SR
calculate_data_units | Given sampling arguments, calculate super set of fleets, years, and data types.
calculate_re | Calculate relative error
case_comp | Write a case file for length- or age-composition data
case_deparse | Turn an argument describing an object into a character.
case_fishing | Write a case file for fishing data to the disk.
case_index | Write a case file for index data to the disk.
case_tv | Write time varying casefiles to the disk
change_data | Change the data that is available as output from an SS operating model.
change_e | Methods to alter which parameters are estimated in a SS3 '.ctl' file.
change_em_binning | Change population and observed length composition bins in an SS estimation model
change_e_fcast_yrs | Check and change forecast file years if necessary
change_f | Alter fishing mortality (_F_) using the SS control file
change_f_par | Alter the fishing mortality (_F_) values in an SS3 '.par' file.
change_lcomp_constant | Set the robustification constant for length composition data.
change_o | Methods to include parameters in an SS3operating model
change_pop_bin | Set up population length bin structure
change_rec_devs | Replace recruitment deviations
change_rec_devs_par | Replace recruitment deviations
change_retro | Alter a starter file for a retrospective analysis
change_tail_compression | Replace tail compression value for length composition data.
change_tv | Methods to include time-varying parameters in an SS3 operating model
check_data | Check that the SS data file looks correct
check_data_str_range | Check input arguments for data
cleanup_ss3 | Clean up after an SS3 run
clean_data | Given sampling arguments remove ("clean") all data in a .dat file that is not specified
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
facet_form | A helper function for building a ggplot facet. Used internally by the plotting functions.
fill_across | Fill in matrix across rows of weight-at-age data by interpolation
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_bin | Get SS3 binary/executable location in package
get_bin_info | Get the parameter values for change_bin
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_nll_components | Get negative log likelihood (NLL) values from a report file list
get_recdevs | Return a set of recruitment deviations
get_results_all | Extract SS3 simulation output
get_results_derived | Extract time series from a model run with the associated standard deviation.
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 Variability About Recruitment Deviations (sigma_R)
get_ss_ver_dl | Get the ss version (either 3.24 or 3.30) from a 'dat_list' list.
get_ss_ver_file | Get the ss version (either 3.24 or 3.30) from an ss file
id_scenarios | Identify ss3sim scenarios within a directory
plot_scalar_boxplot | Print scalar values as boxplots.
plot_scalar_points | Plot scalar values as points.
plot_ts_boxplot | Plot timeseries values as boxplots.
plot_ts_lines | Plot timeseries values as lines.
plot_ts_points | Plot timeseries values as points.
profile_fmsy | Determine Fmsy for a given operating model
remove_CPUE | Remove a q setup line into an SS control file
remove_q_ctl | Remove a q setup line into an SS control file only
rename_ss3_files | Rename SS3-version-specific files
run_ss3model | Run an operating or estimation model for a specified set of scenario IDs
run_ss3sim | Master function to run SS3 simulations
sample_agecomp | Sample age compositions from a Stock Synthesis data file
sample_calcomp | Sample conditional age-at-length (CAL) data and write to file for use by the EM.
sample_comp | Sample composition data from expected values
sample_index | Sample the biomass with observation error
sample_lcomp | Sample length compositions from a Stock Synthesis data file
sample_mlacomp | [BETA VERSION] Sample mean length (size-)-at-age data and write to file for use by the EM.
sample_wtatage | Sample empirical weight-at-age data and write to file for use by the EM
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 function to run an ss3sim simulation
standardize_bounds | Standardize the bounds of the estimation model control file.
substr_r | Substring from right
ts_dat | Example time series data from the ss3sim vignette
vbgf_func | Predict length given VBGF parameters
verify_input | Verify and standardize SS3 input files
verify_plot_arguments | A helper function to check the correct input for the plotting functions.