Assessment data and parameter descriptions

Users need to population a named list containing data inputs and a named list specifying starting values for estimable parameters which are both passed to TMB’s MakeADFun function. This section outlines the elements and corresponding dimensions of both data and parameters.

data

  • ages vector of ages. Length n_ages

  • years vector of years from start year to current year. length n_years

  • length_bins vector of length bin midpoints. length. n_length_bins

  • n_projections_years integer of future years to project the model n_projyears = n_years + n_projections_years

  • do_projection Not implemented

  • n_init_rec_devs number of initial n_age_deviations (parameter$ln_init_rec_dev) to multiply against the initial numbers at age to have non equilibrium initial age-structure. A value of zero will not apply these initial devs and expects parameter$ln_init_rec_dev to have length 1. These deviations are applied equally to both male and female.

  • maturity proportion mature array with dimensions n_ages \(\times\) n_projyears

  • male_mean_weight_by_age male mean weight at age array with dimensions n_ages \(\times\) n_projyears. Units are in kgs, this is because we track millions of fish in the partition, so any weight calculation is in kilo tonnes

  • female_mean_weight_by_age female mean weight at age array with dimensions n_ages \(\times\) n_projyears. Units are in kgs, this is because we track millions of fish in the partition, so any weight calculation is in kilo tonnes

  • M_method 0 = age & time In-variant, 1 = time-varying, 2 = age-varying,

  • male_age_length_transition male age-length transtion matrix for each year. An array with dimensions n_ages \(\times\)n_length_bins \(\times\) n_projyears

  • female_age_length_transition female age-length transtion matrix for each year. An array with dimensions n_ages \(\times\)n_length_bins \(\times\) n_projyears

  • SrType Not implemented

  • historical_jap_fishery_ll_age_length_transition age-length transition for both male and female for early japanese LFs. An array with dimensions n_ages \(\times\)n_length_bins \(\times\) n_projyears

  • proportion_male proportion of males in domestic long-line survey. A value for each year.

  • sigma_R recruitment standard deviation

  • SrType Not implemented

  • spawning_time_proportion vector of proportions that indicate when during the year spawning occurs. Length = n_projyears

  • catch_likelihood 0 is the ADMB formulation, 1 == normal with catch_sd

  • catch_sd catch standard deviation

  • prop_F_hist proportion of fixed gear F to apply during initialisation

  • ll_fishery_catch vector of annual catch for the fixed gear fishery. Units are kilo tonnes

  • trwl_fishery_catch vector of annual catch for the Trawl gear fishery. Units are kilo tonnes

  • loglik_wgt_ll_catch Log-likelihood multiplier

  • loglik_wgt_trwl_catch Log-likelihood multiplier

  • loglik_wgt_Fs Log-likelihood multiplier

  • ll_sel_type vector of integers (one for each time-block) defining the longline fishery selectivity type for each row of ln_ll_sel_m_pars and ln_ll_sel_f_pars

  • ll_sel_by_year_indicator vector of integers (one for each model year) defining the longline fishery selectivity time-block. First ndx needs to be 0

  • trwl_sel_type vector of integers (one for each time-block) defining the trawl fishery selectivity type for each row of ln_ll_sel_m_pars and ln_ll_sel_f_pars

  • trwl_sel_by_year_indicator vector of integers (one for each model year) defining the trawl fishery selectivity time-block. First ndx needs to be 0

  • srv_dom_ll_sel_type vector of integers (one for each time-block) defining the domestic longline survey selectivity type for each row of ln_ll_sel_m_pars and ln_ll_sel_f_pars

  • srv_dom_ll_sel_by_year_indicator vector of integers (one for each model year) defining the domestic longline survey selectivity time-block. First ndx needs to be 0

  • srv_dom_ll_q_by_year_indicator vector of integers (one for each model year) defining the domestic longline survey catchability time-block. First ndx needs to be 0

  • srv_jap_ll_sel_type vector of integers (one for each time-block) defining the domestic Japanese survey selectivity type for each row of ln_ll_sel_m_pars and ln_ll_sel_f_pars

  • srv_jap_ll_sel_by_year_indicator vector of integers (one for each model year) defining the Japanese longline survey selectivity time-block. First ndx needs to be 0

  • srv_jap_ll_q_by_year_indicator vector of integers (one for each model year) defining the Japanese longline survey catchability time-block. First ndx needs to be 0

  • srv_nmfs_trwl_sel_type vector of integers (one for each time-block) defining the NMFS trawl survey selectivity type for each row of ln_ll_sel_m_pars and ln_ll_sel_f_pars

  • srv_nmfs_trwl_sel_by_year_indicator vector of integers (one for each model year) defining the NMFS trawl survey selectivity time-block. First ndx needs to be 0

  • srv_nmfs_trwl_q_by_year_indicator vector of integers (one for each model year) defining the NMFS trawl survey catchability time-block. First ndx needs to be 0

  • srv_jap_fishery_ll_sel_type vector of integers (one for each time-block) defining the early japanese fishery selectivity type for each row of ln_ll_sel_m_pars and ln_ll_sel_f_pars

  • srv_jap_fishery_ll_sel_by_year_indicator vector of integers (one for each model year) defining the early japanese fishery selectivity time-block. First ndx needs to be 0

  • srv_jap_fishery_ll_q_by_year_indicator vector of integers (one for each model year) defining the early japanese fishery catchability time-block. First ndx needs to be 0

  • ll_cpue_q_by_year_indicator vector of integers (one for each model year) defining the longline fishery catchability time-block. First ndx needs to be 0

  • ageing_error_matrix ageing error classifications \(n_{ages} \times n_{ages}\)

  • ll_catchatage_indicator length(ll_catchatage_indicator) = n_years. 1 = calculate catch at age in this year, 0 = don’t calculate catch at age

  • obs_ll_catchatage Longline fishery composition observations dim = n_ages x ll_catchatage_comp

  • ll_catchatage_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • ll_catchatage_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_ll_catchatage scalar log-likelihood multiplier

  • ll_catchatlgth_indicator length(ll_catchatlgth_indicator) = n_years. 1 = calculate catch at length in this year, 0 = don’t calculate catch at age

  • obs_ll_catchatlgth_m Longline fishery length composition observations dim = n_lengths x length(ll_catchatlgth_indicator)

  • obs_ll_catchatlgth_f Longline fishery length composition observations dim = n_lengths x length(ll_catchatlgth_indicator)

  • ll_catchatlgth_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • ll_catchatlgth_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_ll_catchatlgth_f scalar log-likelihood multiplier female longline LF

  • loglik_wgt_ll_catchatlgth_m scalar log-likelihood multiplier male longline LF

  • trwl_catchatlgth_indicator length(trwl_catchatlgth_indicator) = n_years. 1 = calculate catch at length in this year, 0 = don’t calculate catch at age

  • obs_trwl_catchatlgth_m Trawl fishery length composition observations dim = n_lengths x length(trwl_catchatlgth_indicator)

  • obs_trwl_catchatlgth_f Trawl fishery length composition observations dim = n_lengths x length(trwl_catchatlgth_indicator)

  • trwl_catchatlgth_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • trwl_catchatlgth_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_trwl_catchatlgth_m scalar log-likelihood multiplier female trawl LF

  • loglik_wgt_trwl_catchatlgth_f scalar log-likelihood multiplier male trawl LF

  • srv_dom_ll_bio_indicator length(srv_dom_ll_bio_indicator) = n_years. 1 = calculate catch at survey index in this year, 0 = don’t calculate catch at age

  • obs_dom_ll_bio domestic longline survey index observation length = length(srv_dom_ll_bio_indicator)

  • se_dom_ll_bio domestic longline survey index standard errors length = length(srv_dom_ll_bio_indicator)

  • obs_dom_ll_bio_is_numbers integer 0 = weight (biomass), 1 = numbers (abundance)

  • srv_dom_ll_bio_likelihood 0 = ADMB, 1 = lnorm

  • loglik_wgt_srv_dom_ll_bio scalar log-likelihood multiplier survey biomass

  • srv_jap_ll_bio_indicator length(srv_jap_ll_bio_indicator) = n_years. 1 = calculate catch at survey index in this year, 0 = don’t calculate catch at age

  • obs_jap_ll_bio survey Japanese & coopoerative survey index observation length = length(srv_dom_ll_bio_indicator)

  • se_jap_ll_bio survey Japanese & coopoerative survey index standard errors length = length(srv_dom_ll_bio_indicator)

  • obs_jap_ll_bio_is_numbers integer 0 = weight (biomass), 1 = numbers (abundance)

  • srv_jap_ll_bio_likelihood 0 = ADMB, 1 = lnorm

  • loglik_wgt_srv_jap_ll_bio scalar log-likelihood multiplier survey biomass

  • srv_nmfs_trwl_bio_indicator length(srv_nmfs_trwl_bio_indicator) = n_years. 1 = calculate catch at survey index in this year, 0 = don’t calculate catch at age

  • obs_nmfs_trwl_bio NMFS GOA trawl index observation length = length(srv_nmfs_trwl_bio_indicator)

  • se_nmfs_trwl_bio NMFS GOA trawl index standard errors length = length(srv_dom_ll_bio_indicator)

  • obs_nmfs_trwl_bio_is_numbers integer 0 = weight (biomass), 1 = numbers (abundance)

  • srv_nmfs_trwl_bio_likelihood 0 = ADMB, 1 = lnorm

  • loglik_wgt_srv_nmfs_trwl_bio scalar log-likelihood multiplier survey biomass

  • ll_cpue_indicator length(ll_cpue_indicator) = n_years. 1 = calculate catch at survey index in this year, 0 = don’t calculate catch at age

  • obs_ll_cpue NMFS GOA trawl index observation length = length(ll_cpue_indicator)

  • se_ll_cpue NMFS GOA trawl index standard errors length = length(srv_dom_ll_bio_indicator)

  • obs_ll_cpue_is_numbers integer 0 = weight (biomass), 1 = numbers (abundance)

  • ll_cpue_likelihood 0 = ADMB, 1 = lnorm

  • loglik_wgt_ll_cpue scalar log-likelihood multiplier survey biomass

  • srv_jap_fishery_ll_bio_indicator length(srv_jap_fishery_ll_bio_indicator) = n_years. 1 = calculate catch at survey index in this year, 0 = don’t calculate catch at age

  • obs_jap_fishery_ll_bioearly japanese fishery index observation length = length(srv_jap_fishery_ll_bio_indicator)

  • se_jap_fishery_ll_bio early japanese fishery index standard errors length = length(srv_jap_fishery_ll_bio_indicator)

  • obs_jap_fishery_ll_bio_is_numbers integer 0 = weight (biomass), 1 = numbers (abundance)

  • srv_jap_fishery_ll_bio_likelihood 0 = ADMB, 1 = lnorm

  • loglik_wgt_jap_fishery_ll_bio scalar log-likelihood multiplier survey biomass

  • srv_dom_ll_age_indicator length(srv_dom_ll_age_indicator) = n_years. 1 = calculate catch at age in this year, 0 = don’t calculate catch at age

  • obs_srv_dom_ll_age Domestic Longline survey composition observations dim = n_ages x ll_catchatage_comp

  • srv_dom_ll_age_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • srv_dom_ll_age_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_srv_dom_ll_age scalar log-likelihood multiplier

  • srv_dom_ll_lgth_indicator length(srv_dom_ll_lgth_indicator) = n_years. 1 = calculate catch at length in this year, 0 = don’t calculate catch at age

  • obs_srv_dom_ll_lgth_m Domestic Longline survey length composition observations dim = n_lengths x length(srv_dom_ll_lgth_indicator)

  • obs_srv_dom_ll_lgth_f Domestic Longline survey length composition observations dim = n_lengths x length(srv_dom_ll_lgth_indicator)

  • srv_dom_ll_lgth_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • srv_dom_ll_lgth_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_srv_dom_ll_lgth_m scalar log-likelihood multiplier female survey longline LF

  • loglik_wgt_srv_dom_ll_lgth_f scalar log-likelihood multiplier male survey longline LF

  • srv_jap_ll_age_indicator length(srv_jap_ll_age_indicator) = n_years. 1 = calculate catch at age in this year, 0 = don’t calculate catch at age

  • obs_srv_jap_ll_age Domestic Longline survey composition observations dim = n_ages x ll_catchatage_comp

  • srv_jap_ll_age_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • srv_jap_ll_age_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_srv_jap_ll_age scalar log-likelihood multiplier

  • srv_jap_ll_lgth_indicator length(srv_jap_ll_lgth_indicator) = n_years. 1 = calculate catch at length in this year, 0 = don’t calculate catch at age

  • obs_srv_jap_ll_lgth_m Japanese & Co-operative Longline survey length composition observations dim = n_lengths x length(srv_jap_ll_lgth_indicator)

  • obs_srv_jap_ll_lgth_f Japanese & Co-operative Longline survey length composition observations dim = n_lengths x length(srv_jap_ll_lgth_indicator)

  • srv_jap_ll_lgth_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • srv_jap_ll_lgth_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_srv_jap_ll_lgth_m scalar log-likelihood multiplier female survey longline LF

  • loglik_wgt_srv_jap_ll_lgth_f scalar log-likelihood multiplier male survey longline LF

  • srv_jap_fishery_ll_lgth_indicator length(srv_jap_fishery_ll_lgth_indicator) = n_years. 1 = calculate catch at length in this year, 0 = don’t calculate catch at age

  • obs_srv_jap_fishery_ll_lgth Early Japanese fishery length composition observations dim = n_lengths x length(srv_jap_fishery_ll_lgth_indicator)

  • srv_jap_fishery_ll_lgth_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • srv_jap_fishery_ll_lgth_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_srv_jap_fishery_ll_lgth scalar log-likelihood multiplier female survey longline LF

  • srv_nmfs_trwl_age_indicator length(srv_nmfs_trwl_age_indicator) = n_years. 1 = calculate catch at age in this year, 0 = don’t calculate catch at age

  • obs_srv_nmfs_trwl_age NMFS GOA trawl survey composition observations dim = n_ages x ll_catchatage_comp

  • srv_nmfs_trwl_age_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • srv_nmfs_trwl_age_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_srv_nmfs_trwl_age scalar log-likelihood multiplier

  • srv_nmfs_trwl_lgth_indicator length(srv_nmfs_trwl_lgth_indicator) = n_years. 1 = calculate catch at length in this year, 0 = don’t calculate catch at age

  • obs_srv_nmfs_trwl_lgth_m NMFS GOA trawl survey length composition observations dim = n_lengths x length(srv_nmfs_trwl_lgth_indicator)

  • obs_srv_nmfs_trwl_lgth_f NMFS GOA trawl survey length composition observations dim = n_lengths x length(srv_nmfs_trwl_lgth_indicator)

  • srv_nmfs_trwl_lgth_covar_structure 0 = iid, 5 = AR(1), 2 = Unstructured.

  • srv_nmfs_trwl_lgth_comp_likelihood 0 = old multinomial, 1 = TMB’s Multinomial, 2 = dirichlet-multinomial (not implemented)

  • loglik_wgt_srv_nmfs_trwl_lgth_m scalar log-likelihood multiplier female survey NMFS GOA trawl LF

  • loglik_wgt_srv_nmfs_trwl_lgth_f scalar log-likelihood multiplier male survey NMFS GOA trawl LF

  • cpue_q_prior_type integer specifying prior type for cpue (ll fishery index) catchability. 0 = none (uniform), 1 = ADMB version. Needs to be one for each time-block.

  • mu_cpue_q vector specifying the mean for q prior

  • sd_cpue_q vector specifying the standard deviation for q prior

  • srv_jap_fishery_ll_prior_type integer specifying prior type for srv_jap_fishery_ll (early japanese fishery index) catchability. 0 = none (uniform), 1 = ADMB version. Needs to be one for each time-block.

  • mu_srv_jap_fishery_ll_q vector specifying the mean for q prior

  • sd_srv_jap_fishery_ll_q vector specifying the standard deviation for q prior

  • srv_nmfs_trwl_q_prior_type integer specifying prior type for trawl catchability. 0 = none (uniform), 1 = ADMB version. Needs to be one for each time-block.

  • mu_srv_nmfs_trwl_q vector specifying the mean for q prior

  • sd_srv_nmfs_trwl_q vector specifying the standard deviation for q prior

  • srv_jap_ll_q_prior_type integer specifying prior type for japanese longline catchability. 0 = none (uniform), 1 = ADMB version. Needs to be one for each time-block.

  • mu_srv_jap_ll_q vector specifying the mean for q prior

  • sd_srv_jap_ll_q vector specifying the standard deviation for q prior

  • srv_dom_ll_q_prior_type integer specifying prior type for japanese longline catchability. 0 = none (uniform), 1 = ADMB version. Needs to be one for each time-block.

  • mu_srv_dom_ll_q vector specifying the mean for q prior

  • sd_srv_dom_ll_q vector specifying the standard deviation for q prior

  • loglik_wgt_q_priors scalar specifying the log-likelihood weight (multiplier for the priors)

  • M_prior_type integer specifying prior type for japanese longline catchability. 0 = none (uniform), 1 = ADMB version. Needs to be one for each time-block.

  • mu_M vector specifying the mean for q prior

  • sd_M vector specifying the standard deviation for q prior

  • loglik_wgt_M_priors scalar specifying the log-likelihood weight (multiplier for the priors)

  • loglik_wgt_M_regulations scalar specifying the log-likelihood weight for F-devs (multiplier for the priors)

parameters

  • ln_mean_rec scalar of natural logarithm of mean recruitment (units are log millions).
  • ln_rec_dev vector of recruitment deviations, one for each year in the model. I split the ADMB model up into two parameters
  • ln_init_rec_dev Recruitment deviations to apply during initialization they include years before the assessment starts: length = n_init_rec_devs
  • ln_ll_sel_pars array of log selectivity parameters dim = time-blocks, max(sel parameters), n_sex
  • ln_trwl_sel_pars array of log selectivity parameters dim = time-blocks, max(sel parameters), n_sex
  • ln_ll_F_avg scalar for average log fishing mortality
  • ln_ll_F_devs vector of fishing mortality deviations
  • ln_trwl_F_avg scalar for average log fishing mortality
  • ln_trwl_F_devs vector of fishing mortality deviations
  • ln_ll_cpue_q vector of log catchabilities parameters for cpue observation. length = time-blocks
  • ln_srv_jap_fishery_ll_q vector of log catchabilities parameters for srv_dom_ll observation. length = time-blocks
  • ln_srv_jap_fishery_ll_sel_pars array of log selectivity parameters dim = time-blocks, max(sel parameters): NOTE not sex disaggregated!! no sex dimension
  • ln_srv_nmfs_trwl_q vector of log catchabilities parameters for NMFS bottom trawl survey observation. length = time-blocks
  • ln_srv_nmfs_trwl_sel_pars array of log selectivity parameters dim = time-blocks, max(sel parameters), n_sex
  • ln_srv_jap_ll_q vector of log catchabilities parameters for japanese longline survey observation. length = time-blocks
  • ln_srv_jap_ll_sel_pars array of log selectivity parameters dim = time-blocks, max(sel parameters), n_sex
  • ln_srv_dom_ll_q vector of log catchabilities parameters for Domestic longline survey observation. length = time-blocks
  • ln_srv_dom_ll_sel_pars array of log selectivity parameters dim = time-blocks, max(sel parameters), n_sex
  • ln_M scalar log of parameter
  • ln_M_year_devs vector of log year deviations
  • ln_M_age_devs vector of log age deviations