| age_to_len | Convert numbers at age to numbers at length |
| catch.in.biomass | Converts catch in numbers to catch in biomass |
| catch.in.number | Calculates numbers at age of catch |
| check_convergence | Check for SS convergence |
| competition_fun | Convert numbers at age to numbers at length |
| copy_files | Copy assessment files to a new folder |
| dat.update | This takes simulated data from the operating model pop... |
| exploit_catch | Calculates catch-at-age by fleet based on exploitation rates |
| find_spr | Find the SPR input value for forecast.ss file to achieve SPR... |
| getRP | Get reference point values after assessment run |
| H_rate | Function to solve for harvest(exploitation) rate of a fleet... |
| jit_for_converg | Run jitter analysis if model didn't converge |
| MO_SSoutput | A function to create a list object for the output from Stock... |
| MO_writeforecast | write forecast file |
| Numextract | Extract multiple numbers from a character string |
| num_to_bio | Converts numbers-at-age to biomass-at-age or vice versa.... |
| p_star | Find the acceptable probability of going past the OFL (P*) |
| rand_intvect | This creates a vector of N whole numbers that add up to M. |
| rand_vect_cont | This creates a vector of N numbers that add up to M (can be... |
| rebuild_f | Find the catch and f for time t_target required to rebuild... |
| rebuild_ttarg | Find the time it takes to rebuild the stock once SSB is below... |
| run_ss | This runs SS and returns TRUE if there was an error that... |
| simAgecomp | Generates age composition data from simulated catches |
| simBatage | Calculates biomass at age for fishery dependent surveys |
| simBatlen | Calculates biomass at age for fishery independent surveys |
| simCompetition | Generates competition index based on relative Red Snapper... |
| simIndex | Generates indices of abundance based on simulated catch |
| solve_for_f | Function to solve for F by fleet based on catch for that year |
| splt.recombine | General use functions for data generation and manipulation |
| theme_pub | Publication style ggplot theme |
| try_jit | This runs a jitter for ss if the model does not converge.... |
| zatage | Calcualte total mortality at age |
