Fisheries Stock Assessment Simulation Testing with Stock Synthesis

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Documentation for package ‘ss3sim’ version 1.0.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.