Man pages for ss3sim/ss3sim
Fisheries Stock Assessment Simulation Testing with Stock Synthesis
| 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,... |
| calculate_bias | Calculate bias adjustment for recruitment deviations |
| calculate_data_units | Calculate fleets, years, and data types needed given sampling... |
| 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... |
| change_data | Change the data that is available from a list object |
| change_dat_bin | Change the bins for a composition object |
| change_e | Methods to alter the parameters estimated in a Stock... |
| change_em_binning | Change population and observed length-composition bins |
| change_f | Specify fishing mortality, F, using the Stock Synthesis... |
| change_lcomp_constant | Set the robustification constant for length-composition data |
| change_o | Methods to include parameters in a Stock Synthesis operating... |
| 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... |
| 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... |
| 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... |
| 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... |
| get_model_folder | Get the folder location of an included Stock Synthesis 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 Stock Synthesis simulation output |
| get_results_derived | Extract time series from a model run with the associated... |
| 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 |
| lists2df | Combine multiple lists element wise to a single data frame |
| make_df | Make a list of lists with dataframe components into a... |
| 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... |
| sample_mn | Sample with a multinomial distribution |
| sample_wtatage | Sample empirical weight-at-age data |
| scalar2list | Replicate an object a number of times to return a list |
| 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... |
| setup_scenarios_name | Create a name for an unnamed scenario |
| ss3sim_base | High-level wrapper to run a simulation |
| ss3sim-deprecated | Deprecated functions in package 'ss3sim' |
| ss3sim-package | ss3sim: Fisheries stock assessment simulation testing with... |
| 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... |
