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aav()
Average Annual Variation (AAV)
abi()
Compute Age-Based Indicator
as_scalar_threshold_f()
Threshold HCR with Fmax scaled by Age Structure
average_abi()
Compute Average ABI across projection period
average_age()
Compute Average Age across projection period
average_annual_catch_variation()
Compute Average Annual Catch Variation (AAV) across projection period
average_annual_dynamic_value()
Compute Average Annual Dynamic Value of Catch across projection period
average_annual_value()
Compute Average Annual Value of Catch across projection period
average_catch()
Compute Average Catch across projection period
average_proportion_biomass_old()
Compute average proportion of population that is "Old" across projection period
average_proportion_catch_large()
Compute average proportion of catch that is "Large" across projection period
average_ssb()
Compute Average SSB across projection period
beverton_holt()
Beverton-Holt stock recruitment relationship #' Defines a function factory for yieding recruitment from a Bevrton-Holt stock recruitment relationship, parameterized using steepeness. Initial call to this function sets up a new function that takes the current SSB as input, and returns the predicted recruitment from the BH SRR defined by h, R0, and S0.
bind_mse_outputs()
Create Tibble of MSE Output Data from Multiple Models
biomass_crash_time()
Compute number of years requied for SSB to crash
biomass_recovery_time()
Compute number of years requied for SSB to recover
calculate_joint_selret()
Calculate Joint Selectivity and Retention Across Multiple Fleets
calculate_npfmc_ref_points()
Calculate NPFMC groundfish reference points
calculate_ref_points()
Calculate SPR Based Reference Points
compute_average_age()
Compute average age of a population
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
extend_3darray_last_dim()
Extend a 3D array along its final dimension
extend_vec_last_val()
Extend a vector by copying its final value
filter_hcr_om()
Filter processed MSE data to a subset of HCRs and OMs
filter_times()
Filter processed MSE data to between two time points,
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
generate_annual_frequency()
Generate frequency vector
get_atage_groups()
Get Catch or Numbers-at-Age by Age Groups
get_b40_timeseries()
Get Timeseries of B40 from MSE Simulations
get_big_recruitment_filter()
Create dplyr Filter for Years Around Large Recruitment Events
get_fishing_mortalities()
Get Annual Fishing Mortality
get_hcrphase_data()
Get HCR recommended F and SSB data for Phaseplane Plot
get_landed_catch()
Get Landed Catches
get_management_quantities()
Get ABC, TAC, and Expected Landings
get_phaseplane_catch_data()
Get Catch and SSB data for Phaseplane Plot
get_phaseplane_data()
Get F and SSB data for Phaseplane Plot
get_recruits()
Get Annual Recruits
get_reference_points()
Get Reference Points from MSE Simulations
get_saved_model_runs()
Load Saved MSE Model Runs from Disk
get_ssb_biomass()
Get Spawning Biomass and Total Biomass
inf_max()
Get maximum value without considering infinite values
npfmc_tier3_F()
Compute F from Tier 3 HCR
performance_metric_summary()
Compute all Performance Metrics
prop_fully_mature()
Compute proportion of population that is fully mature
prop_low_biomass()
Compute proportion of years SSB is below a threshold level across projection period
prop_mature()
Compute proportion of a population that is mature
prop_years_catch()
Compute proportion of years catch exceeds a threshold level across projection period
recruits_crash()
Recruitment function with a specified crash period
reformat_ggdist_long()
Change a `ggdist` Tibble to Long Format
regime_recruits()
Regime-like recruitment
resample_recruits()
Resample recruitment from historical timeseries #' Resample, with replacement, the historical recruitment timeseries.
resample_regime_recruits()
Regime-like recruitment #' Generate future recruitment timeseries based on historcial regime-like recruitment dynamics. Historical recruitments identified as having belonged to a specific regime are randomly resampled, with replacement.
round_to_zero()
Round dataframe column to Zero
run_EM()
Run Estimation Method
run_mse()
Run Management Strategy Evaluation
run_mse_multiple()
Run MSE Simulations Across OMs and HCRs
sable_om
Default Operating Model for Alaska Sablfish
scale_and_rank()
Scale and Rank dataframe columns within groups
setup_hcr_options()
Setup HCR Objects
setup_mp_options()
Setup Management Procedure Object
shannon_diversity()
Compute Shannon Diversity Index (H')
simulate_TAC()
Simulate Total Allowable Catch Projections
simulate_em_data()
Simulate OM Observation Data for TMB Assessment Model
simulate_em_data_sex_disaggregate()
Simulate OM Observation Data for Sex-Disaggregated TMB Assessment Model
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
stairstep_attainment()
Stairstep Attainment Function
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.
total_catch()
Compute Total Catch over projection period