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. |