Fisheries Stock Assessment Simulation Testing with Stock Synthesis


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Documentation for package ‘ss3sim’ version 0.9.3

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ss3sim-package ss3sim: Fisheries stock assessment simulation testing with Stock Synthesis
add_nulls Add NULL values to non-existent list elements
bias_ss3 Perform a single bias adjustment run
calculate_data_units Given sampling arguments, calculate super set of fleets, years, and data types.
calculate_re Calculate relative error
calculate_runtime Calculate run time
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_agecomp (Depreciated) Sample age compositions from expected values
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_f Alter the fishing mortality (_F_) values in an SS3 '.par' file.
change_fltname Standardize column name for FltSvy in event 'r4ss' is not the newest version.
change_index (Depreciated) Sample the biomass with observation error
change_lcomp (Depreciated) Sample length compositions from expected values
change_lcomp_constant Set the robustification constant for length composition data.
change_maturity Alter a control file to specify the SS3 maturity option
change_rec_devs 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
change_year Methods to change the years in an ss3sim model
check_data Check that the SS3 data file looks correct
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
extract_expected_data Extract the expected data values
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 recruitment deviation sigma
id_scenarios Identify ss3sim scenarios within a directory
pastef Paste with "/" as the separator
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
rename_ss3_files Rename SS3-version-specific files
run_bias_ss3 Determine level of bias adjustment for SS3 runs
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 expected values
sample_calcomp Sample conditional age-at-length (CAL) data and write to file for use by the EM.
sample_index Sample the biomass with observation error
sample_lcomp Sample length compositions from expected values
sample_mlacomp [BETA VERSION] Sample mean length (size-)-at-age data and write to file for use by the EM.
sample_wtatage Sample empirial 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.