Man pages for 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,... |
| calculate_data_units | Given sampling arguments, calculate super set of fleets,... |
| 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... |
| change_e | Methods to alter which parameters are estimated in a SS3... |
| change_e_fcast_yrs | Check and change forecast file years if necessary |
| change_em_binning | Change population and observed length composition bins in an... |
| change_f | Alter fishing mortality (_F_) using the SS control file |
| change_f_par | Alter the fishing mortality (_F_) values in an SS3 '.par'... |
| 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... |
| check_data | Check that the SS data file looks correct |
| check_data_str_range | Check input arguments for data |
| clean_data | Given sampling arguments remove ("clean") all data in a .dat... |
| cleanup_ss3 | Clean up after an SS3 run |
| copy_ss3models | Copy the operating and estimation models and create a folder... |
| 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... |
| fill_across | Fill in matrix across rows of weight-at-age data by... |
| get_args | Take a csv file, read it, and turn the first column into the... |
| 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... |
| get_nll_components | Get negative log likelihood (NLL) values from a report file... |
| 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... |
| 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'... |
| 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... |
| 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... |
| 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... |
| sample_wtatage | Sample empirical weight-at-age data and write to file for use... |
| sanitize_admb_options | Check admb options to make sure there aren't flags there... |
| scalar_dat | Example scalar data from the ss3sim vignette |
| setup_parallel | Setup parallel processing |
| ss3sim | ss3sim: Fisheries stock assessment simulation testing with... |
| 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... |
