add_CPUE                Add a q setup line into an SS control file
add_colnames            Create matching column names across a list of
                        data frames
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_e_fcast_yrs      Check and change forecast file years if
                        necessary
change_em_binning       Change population and observed length
                        composition bins in an SS estimation model
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
clean_data              Given sampling arguments remove ("clean") all
                        data in a .dat file that is not specified
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
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.
