Package index • afscOM

All functions
`F_to_mu()`	instantaneous rate to harvest rate
`apply_harvest_control_rule()`	Apply a harvest control rule
`apportion_catch()`	Apportion Catch
`apportion_recruitment()`	Apportion Recruitment
`apportion_recruitment_single()`	Apportion Recruitment Single
`baranov()`	Baranov Catch Equation
`beverton_holt()`	Beverton-Holt Stock Recruit Relationship
`calculate_joint_selret()`	Calculate Joint Selectivity and Retention Across Multiple Fleets
`calculate_npfmc_ref_points()`	Calculate NPFMC groundfish reference points
`calculate_spr_refpoints()`	Calculate F/B Reference Points via SPR Methods
`catch_at_age()`	Catch-at-age
`compute_bio()`	Compute Total Stock Biomass
`compute_bx()`	Compute average SSB under a level of F
`compute_fleet_catch()`	Compute Catch by Fishing Fleet
`compute_fx()`	Find F that yields a given SPR
`compute_sbpr()`	Compute Spawning Biomass per Recruit (SBPR)
`compute_spr()`	Compute Spawning Potential Ratio (SPR)
`compute_ssb()`	Compute Spawning Stock Biomass
`compute_total_catch()`	Compute Total Catch
`compute_total_f()`	Compute Total Fishing Mortality
`constant_catch_hcr()`	Constant Catch Harvest Control Rule
`constant_f_hcr()`	Constant Fishing Mortality Harvest Control Rule
`cyclic_recruitment()`	Generate log-recruitment from two defined regimes of a specified length
`discard_F()`	Discarded Fishing Mortality Rate
`extend_years()`	Extend demographic parameter matrices to more years
`findF_bisection()`	Find F given a desired level of catch
`find_F()`	Find F given a desired level of catch
`generate_output_matrices()`	Generate output matrices
`generate_param_matrix()`	Generate a filled parameter matrix
`get_annual_recruitment()`	Get Annual Recruitment
`get_model_dimensions()`	Obtain model dimensions from parameter matrix
`good_dem_matrices`	good_dem_matrices
`kapur2024_sablefish_data`	kapur2024_sablefish_data
`listN()`	Set variable names as names of list
`mu_to_F()`	harvest rate to instantaneous
`plot_atage()`	Plot Numbers at age
`plot_bio()`	Plot Total biomass
`plot_catch()`	Plot Catch
`plot_demographic_parameters()`	Plot demographic parameters
`plot_f()`	Plot Fishing mortality biomass
`plot_mat()`	Plot Maturity-at-Age
`plot_mort()`	Plot Mortality
`plot_selret()`	Plot Selectivity-at-Age and Retention-at-Age
`plot_ssb()`	Plot Spawning stock biomass
`plot_waa()`	Plot Weight-at-Age
`project()`	Project Population Forward Multiple Years
`project_single()`	Project population forward by 1 year
`raw_sablefish_dem_params`	raw_sablefish_dem_params
`resample_recruitment()`	Resample from historical recruitment timeseries
`retained_F()`	Retained Fishing Mortality Rate
`sablefish_assessment_data`	Sablefish assessment
`sablefish_dem_params`	Demographic parameter matrices for Alaska Sablefish
`set_model_params()`	Setup model parameters
`setup_model_options()`	Set Default Values for Model Options
`simple_om`	OM Components for a Simple Simulation
`simple_om_spatial`	simple spatial OM example
`simulate_ac()`	Simulate survey age composition data
`simulate_caa()`	Simulate catch-at-age composition data
`simulate_catch()`	Simulate catches in one region during on year
`simulate_lognormal_obs()`	Simulate observations from a lognormal distribution #' A wrapper function around `rlnorm` that generates a single random observation from a lognormal distribution centered on a predicted value (`pred`) and given a level of error (`cv`).
`simulate_multinomial_obs()`	Simulate observations from a multinomial distribution #' A wrapper function around `rmultinom` that generates a single vector of observations from a multinomial distribution where each of the `K` multinomial classes has probability `pred`. This function will automatically handle generating multinomial draws across multiple sexes. Aging error can be optionally applied.
`simulate_observations()`	Simulate Observations from Fisheries and Surveys
`simulate_population()`	Project an Age Structure Population Forward by 1 year #' Description
`simulate_rpn()`	Simulate Relative Population Numbers Index
`simulate_rpw()`	Simulate Relative Population Weight Index
`spatial_sablefish_assessment_data`	Spatial Sablefish Assessment
`subset_dem_params()`	Subset demographic parameter matrices by first dimensions
`subset_matrix()`	Subset matrix of undetermined dimensions
`threshold_f_hcr()`	Threshold Fishing Mortality Harvest Control Rule
`update_output_matrices()`	update matrices
`validate_dem_params()`	Validate Demographic Parameter Matrices

Reference

All functions