Function reference

All functions

abi()

Compute Age-Based Indicator #' Compute ABI (Griffiths et al. 2023) given a population age structure and an age structure to use as a reference.

as_scalar_threshold_f()

Threshold HCR with Fmax scaled by Age Structure

average_age()

Compute average age of a population #' Calculate the average age of a population given its age structure.

bind_mse_outputs()

Create Tibble of MSE Output Data from Multiple Models

calculate_ref_points()

Calculate NPFMC groundfish reference points

compute_bx()

Compute average SSB under a level of F

compute_sbpr()

Compute Spawning Biomass per Recruit (SBPR)

compute_spr()

Compute Spawning Potential Ratio (SPR)

constant_F()

Compute F from a constant F rule

fit_TMB_model()

Fit the SpatialSablefishAssessment TMB Model #' Use Template Model Builder (TMB) to fit the assessmnte model from `SpatialSablefishAssessment`. Note that the 'ln_M_year_devs' and 'ln_M_age_devs' parameters have been turned off.

format_em_data()

Format OM Observation Data for TMB Assessment Model #' Format data and observations from an `afscOM` operating model and update the model data and parameters required by the `SpatialSablefishAssessment` TMB assessment model.

npfmc_tier3_F()

Compute F from Tier 3 HCR

prop_fully_mature()

Compute proportion of population that is fully mature #' Calculate the proportion of a population in age classes that are "fully mature" (e.g. mat > 0.995).

prop_mature()

Compute proportion of a population that is mature

reformat_ggdist_long()

Change a `ggdist` Tibble to Long Format #' Description

run_mse()

Run Management Strategy Evaluation #' Run an MSE simulation loop.

run_mse_multiple()

Run Multiple MSE Simulations #' Wrapper function around `run_mse` that handle running and compiling the outputs of multiple MSE closed-loop simulations, across different random seeds.

shannon_diversity()

Compute Shannon Diversity Index (H')

simulate_TAC()

Simulate Total Allowable Catch Projections #' Determine the total allowable catch (TAC) in the next simulation year based on the fishing mortality rate identified by a harvest control rule (HCR). TAC is computed by projecting the population forward one year under the specific level of F and computing the the amount of catch that would be taken from that projected population structure based on the joint fishery selectivity curve.

spr_x

Find F that yields a given SPR spr_x(nages, mort, mat, waa, sel, ret, target_x = 0.35) nagesnumber of ages in age structure mortinstantaneous natural mortality rate matmaturity-at-age vector waaweight-at-age vector seltotal selectivity-at-age vector rettotal retention-at-age vector target_xdesired SPR proportion Use bisection algorithm to identify the level of fishing mortality required to yield an SPR of x

threshold_cap()

Compute F following a threshold rule, with a cap at B/B_ref = 1

threshold_f()

Generic threshold F harvest control rule #' A generic 4 parameters threshold F HCR.