Function reference • ss3sim

All functions
`add_colnames()`	Create matching column names across a list of data frames
`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_bias()`	Calculate bias adjustment for recruitment deviations
`calculate_data_units()`	Calculate fleets, years, and data types needed given sampling parameters
`calculate_re()`	Calculate relative error
`change_catch()`	Change catch in the Stock Synthesis data list
`change_comp()`	Change composition data to dummy data for running the operating model
`change_dat_bin()`	Change the bins for a composition object
`change_data()`	Change the data that is available from a list object
`change_e()`	Methods to alter the parameters estimated in a Stock Synthesis model
`change_em_binning()`	Change population and observed length-composition bins
`change_f()`	Specify fishing mortality, \(F\), using the Stock Synthesis control file
`change_lcomp_constant()`	Set the robustification constant for length-composition data
`change_o()`	Methods to include parameters in a Stock Synthesis operating model
`change_pop_bin()`	Set up population length bin structure
`change_q()`	Adds or removes catchability parameters from a control file
`change_rec_devs()`	Replace recruitment deviations
`change_recyear()`	Change start year main recruitment deviations in control file
`change_retro()`	Alter a starter file for a retrospective analysis
`change_startyear()`	Change start year of the data file
`change_tail_compression()`	Replace tail compression value for length composition data
`change_tv()`	Methods to include time-varying parameters in a Stock Synthesis operating model
`change_year()`	Change the years estimated
`check_data()`	Check that the Stock Synthesis data file looks correct
`check_data_str_range()`	Check input arguments for data
`check_eqlength()`	Check if input arguments have the same length
`check_forecast()`	Check input forecast file values
`check_q()`	Check if desired \(q\) parameters exist in control file list
`clean_data()`	Given sampling arguments, remove unneeded data from a .dat file
`codemctl`	Control file for the cod estimation method
`codomctl`	Control file for the cod operating model
`codomdat`	Data for the cod operating model
`convert_to_wide()`	Convert long-style ss3sim output to wide format
`copy_ss3models()`	Copy the OM or EM into a scenario directory
`create_em()`	Create an EM from an OM
`create_logo()`	Create the ss3sim logo
`facet_form()`	Helper function for building a ggplot facet
`fill_across()`	Fill in matrix across rows of weight-at-age data by interpolation
`find_position()`	Find integer reference to fleet names
`get_bin()`	Get Stock Synthesis binary/executable location
`get_compfit()`	Get summaries of fits to composition data from report file list
`get_model_folder()`	Get the folder location of an included Stock Synthesis 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 Stock Synthesis simulation output
`get_results_derived()`	Extract time series from a model run with the associated standard deviation.
`get_results_iter()`	Get results for 1 iteration
`get_results_mod()`	Get results for 1 model run
`get_results_scalar()`	Extract scalar quantities from a model run.
`get_results_scenario()`	Extract Stock Synthesis simulation results for one scenario
`get_results_timeseries()`	Return the time series information from an iteration
`get_scenarios()`	Identify scenarios in `directory`
`get_sigmar()`	Get Variability About Recruitment Deviations (\(\sigma_R\))
`get_success()`	Determine if a Stock Synthesis run was successful
`make_df()`	Make a list of lists with dataframe components into a dataframes
`plot_boxplot()`	Plot results of a simulation as boxplots
`plot_cummean()`	Plot the cumulative mean for a parameter
`plot_lines()`	Plot time-series values as lines
`plot_points()`	Plot results of a simulation as a scatterplot
`plot_ss3sim()`	Base plot for `ss3sim` data
`profile_fmsy()`	Determine Fmsy for a given operating model
`replace_x()`	Replace a `NULL` value with `NA` in a list
`run_ss3sim()`	Master function to run a set of simulations using ss3sim
`sample_agecomp()`	Sample age compositions from a Stock Synthesis data file
`sample_calcomp()`	Sample conditional age-at-length data
`sample_catch()`	Sample the catches with observation error
`sample_comp()`	Sample composition data from expected values
`sample_discard()`	Sample the discard with observation error
`sample_dm()`	Sample with a Dirichlet-Multinomial distribution
`sample_index()`	Sample the CPUE/index data with observation error
`sample_lcomp()`	Sample length compositions from a Stock Synthesis data file
`sample_lognormal()`	Sample observations using log-normal error corrected for bias
`sample_mlacomp()`	BETA VERSION Sample mean length (size-)-at-age data and write to file for use by the EM
`sample_mn()`	Sample with a multinomial distribution
`sample_wtatage()`	Sample empirical weight-at-age data
`scalar_dat`	Example scalar data from the Introduction vignette
`setup_bins()`	Set up bin structure for composition data
`setup_parallel()`	Setup parallel processing
`setup_scenarios()`	Get scenario information from a data frame of specifications
`setup_scenarios_defaults()`	Set up a generic scenario
`setup_scenarios_fleet()`	Set up fleet-specific information
`setup_scenarios_lookup()`	Create a named vector to look up full names for types of arguments
`setup_scenarios_name()`	Create a name for an unnamed scenario
`ss3sim_base()`	High-level wrapper to run a simulation
`standardize_sampling_args()`	Check and standardize list components of sampling functions
`ts_dat`	Example time-series data from the Introduction vignette
`verify_input()`	Verify and standardize Stock Synthesis input files
`verify_plot_arguments()`	Helper function for ensuring correct input for the plotting functions

Reference

All functions