In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Overview

Update Stock Synthesis software
Update fishery catch and age-composition data in 2 stages:
Small updates to years prior to r last_assess_yr
Add new data for r last_assess_yr
Update survey biomass estimate and age data in 2 stages:
Small updates to years prior to r last_assess_yr
Add new r last_assess_yr survey index point
Update and add new r last_assess_yr weight-at-age data
Weight-at-age data now come from a model with age, sex, year, and cohort as inputs
Maturity-at-age data now come from a spatio-temporal model with age, day of year, and ocean temperature as inputs
Update the age-1 index time series
Add new r last_assess_yr index point
All models run using MCMC

The median estimate of r end_yr relative spawning biomass is r curr_depl_median% (with 95% interval from r curr_depl_lower% to r curr_depl_upper%)
The 2020 and 2021 cohorts make up a large fraction of coastwide catches
2014 and 2016 cohorts estimated to be above average
2015, 2018, and 2019 cohorts estimated to be below average
2020 cohort estimated to be slightly above average
2021 cohort potentially large (with high uncertainty)
Default harvest rule estimated median catch limit for r min(forecast_yrs) is r ct_limit_quantiles["median"] t (with 95% interval from r ct_limit_quantiles["lower"] to r ct_limit_quantiles["upper"] t)
New r last_data_yr age data from fishery and survey are fit well by the model
Coastwide catch in r end_yr-1 was r last_yr_landings t, out of a TAC (adjusted for carryovers) of r last_yr_tac t
Attainment in the U.S. was r last_yr_us_attained% of its quota (r paste0(ifelse(last_2yr_us_attained_diff < 0, "down", "up")) r abs(as.numeric(last_2yr_us_attained_diff))% from last year); in Canada it was r last_yr_can_attained% (r paste0(ifelse(last_2yr_can_attained_diff < 0, "down", "up")) r abs(as.numeric(last_2yr_can_attained_diff))% from last year)