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