Package index • sbt

Simulated example

Public simulated model data and its fitted maximum-likelihood example.

sbt_example_data(): Load the bundled simulated SBT assessment data
sbt_example_simulate(): Simulate the bundled public SBT example
sbt_example_fit(): Load the bundled simulated SBT maximum-likelihood fit

Saved model fits

Functions for saving, validating, sharing, and rebuilding fitted models.

sbt_fit(): Create a staged, portable SBT model fit
sbt_add_parameters(): Add or override SBT model parameters
sbt_add_priors(): Add SBT model priors
sbt_add_map(): Add an RTMB parameter map
sbt_add_bounds(): Add optimizer bounds
sbt_add_random(): Add an RTMB random-effect specification
sbt_add_makeadfun_args(): Add extra RTMB MakeADFun arguments
sbt_build_object(): Build the RTMB objective for an SBT fit
sbt_optimise(): Optimise a staged SBT fit
sbt_add_optimisation(): Attach an existing optimization result to a staged SBT fit
sbt_mcmc(): Run MCMC for a staged SBT fit
sbt_add_mcmc(): Attach an existing MCMC result to an SBT fit
sbt_add_msy(): Add MSY calculations to an SBT fit
sbt_obj(): Access the runtime objective for a portable SBT fit
sbt_fit_report(): Recreate the fitted model report
sbt_fit_validation(): Inspect an embedded SBT fit-validation record
sbt_fit_validate(): Validate a portable SBT fit
sbt_fit_compatibility(): Check whether an SBT fit can be rebuilt by the current package
sbt_fit_save() sbt_fit_read(): Save and read portable SBT fits
sbt_fit_rebuild(): Rebuild an RTMB object from a portable SBT fit
sbt_fit_upgrade(): Explicitly upgrade an older SBT fit
as_tmbfit(): Convert stored posterior draws to a SparseNUTS-style fit
add_posterior_summaries(): Add posterior report summaries to an SBT fit
get_posterior_summary(): Extract an embedded posterior summary

Functions

Functions for model building, fitting, and inference.

check_abundance(): Check abundance outputs
check_bounds(): Check if parameters are up against the bounds
check_estimability(): Check for identifiability of fixed effects
check_mcmc(): Check a fitted SBT posterior
check_mle(): Check a fitted SBT maximum-likelihood estimate
check_sliced(): Check sliced age frequencies used by direct removals
cmb(): Bind the data argument of a two-argument function
do_dynamics(): Population dynamics
biological_state_contract(): Biological-state acceptance contract
biological_state_passes(): Test whether biological-state diagnostics pass
diagnose_sbt_states(): Diagnose biological states over an MLE or posterior
evaluate_priors(): Evaluate priors
expand_parameter_names(): Expand repeated RTMB parameter names
extract_fixed(): Extract fixed effects
find_msy(): Find MSY for one prepared model state
get_aerial_survey_like(): Aerial survey likelihood
get_age_like(): Age composition likelihood
get_bounds(): Get default parameter bounds
get_cpue_length_like(): CPUE length composition likelihood
get_cpue_like(): CPUE index likelihood
get_data(): Prepare SBT assessment model data
get_dl(): Obtain dl
get_GT_like(): Genetic tagging likelihood
get_harvest_rate(): Harvest rate calculation
get_harvest_wall_penalty(): Smooth preventive harvest-wall contribution
get_HSP_like(): Half-sibling pair likelihood
get_initial_numbers(): Initial numbers and Beverton-Holt parameters
get_length_at_age(): Obtain the length at age array
get_length_like(): Length Composition Likelihood
get_loo(): Obtain the leave-one-out information criterion (LOO IC)
get_M_length(): Natural mortality at length
get_M(): Natural mortality at age
get_map(): Get default parameter mapping
get_parameters(): Get default initial parameter values
get_phi(): Spawning output-at-age
get_POP_like(): Parent-Offspring Pairing Likelihood
get_posterior(): Obtain samples from the posterior distribution of reported quantities
get_priors(): Get priors
get_recruitment(): Calculate recruitment
get_recruitment_prior(): Recruitment prior
get_rho(): Estimate temporal autocorrelation in recruitment deviations
get_sel_list(): Get list of selectivity parameters
get_selectivity(): Compute selectivity-at-age by year
get_selectivity_prior(): Selectivity prior
get_sliced_afs(): Obtain sliced age frequencies from length frequencies
get_tag_like(): Tag-recapture likelihood
get_troll_like(): Troll CPUE likelihood
get_weight_at_age(): Obtain the mean weight at age
make_parameter_table(): Make a table of estimated model parameters
mar(): Median of the absolute residual (MAR)
msy_calc(): Equilibrium MSY for the SBT fishery structure
run_msy(): Run annual MSY over an SBT posterior
pairs_rtmb(): Pair plots for RTMB MCMC fits
posfun(): Positive Constraint Penalty Function
priors_to_math(): Convert prior specifications to LaTeX equations
repair_af_slices_weighted(): Repair empty sliced AFs for catch slices.
harvest_wall_contract(): Preventive harvest-wall contract
sbt_globals(): Functions required by the SBT RTMB objective
sbt_model(): Southern bluefin tuna assessment objective
sbtprofile(): Adaptive likelihood profiling
sdnr(): Standard deviation of the normalised residual (SDNR)
summarise_biological_state(): Summarise biological feasibility of one model report
sel_rho_to_par() sel_rho_from_par(): Transform selectivity autocorrelation parameters

Plots

Functions for visualising model outputs.

plot_aerial(): Plot aerial survey fit
plot_aerial_residuals(): Plot aerial survey residuals
plot_af(): Plot age frequency
plot_af_residuals(): Plot age-composition OSA residuals
plot_biomass_spawning(): Plot total reproductive output
plot_catch(): Plot catch
plot_cpue(): Plot CPUE
plot_cpue_residuals(): Plot CPUE residuals
plot_dist_length_at_age(): Plot the distribution of length at age
plot_gt(): Plot gene-tagging (GT) matches
plot_gt_residuals(): Plot GT residuals
plot_hrate(): Plot harvest rate
plot_hsps(): Plot close-kin match fits
plot_hsps_residuals(): Plot HSP residuals
plot_initial_numbers(): Plot initial numbers
plot_length_at_age(): Plot length at age
plot_levs(): Plot LEV grid posterior pairs
plot_lf(): Plot LF
plot_lf_residuals(): Plot length-composition OSA residuals
plot_loo(): Plot PSIS LOO
plot_natural_mortality(): Plot natural mortality
plot_paly(): Plot PALY age-length probabilities
plot_pops(): Plot POP fits
plot_pops_residuals(): Plot POP residuals
plot_prior_posterior(): Plot prior and posterior distributions
plot_profile(): Plot likelihood profiles
plot_rec_devs(): Plot recruitment deviates
plot_recruitment(): Plot recruitment
plot_selectivity(): Plot selectivity
plot_sliced_afs(): Plot sliced AFs
plot_tags(): Plot tags
plot_tags_fits_pooled(): Plot pooled conventional-tag fits
plot_tags_recaptures_pooled(): Plot total conventional-tag recaptures by release year
plot_tags_residuals(): Plot tag recapture residuals
plot_troll(): Plot troll index
plot_troll_residuals(): Plot troll survey residuals
plot_weight_at_age(): Plot weight at age

Grid workflows

Current deterministic and posterior grid construction, validation, sampling, and conversion.

make_mle_grid_parameters(): Build parameter inputs for an MLE grid
run_grid(): Run a grid
summarise_mle_grid(): Summarise fitted MLE-grid cells
validate_mle_grid_state_records(): Validate saved MLE-grid state records
sample_grid(): Sample from the grid
grid_to_tmbfit(): Convert sampled grid to a tmbfit object
run_grid_mcmc(): Run a grid of MCMCs
select_balanced_grid_iters(): Select balanced rows from a combined grid sample
grid_mcmc_to_tmbfit(): Convert a grid of MCMC cells to a tmbfit object

Projections

Functions for constructing inputs, schedules, and closed-loop assessment projections.

run_projections(): Run CTP projections
project_ctp_schedule(): Build the CTP projection TAC schedule
project_rec_devs(): Project recruitment deviates
project_selectivity(): Project selectivity
extend_hsp_cohorts(): Extend HSP data set

Cape Town procedure

Public Cape Town procedure controls and the default data object.

sbt_ctp_controls() mpdat: Cape Town procedure controls and default data object

Legacy grid compatibility

Compatibility helpers for historical direct-anchor in-memory grids.

get_grid(): Set up a legacy direct-anchor grid
rerun_grid(): Run a grid again
check_grid(): Check estimability of the grid

Legacy ADMB comparison model

Functions used only by the sbt_vs_admb comparison vignette.

sbt_model_v1(): The sbt model
get_data_v1(): Set up the data input file
get_dl_v1(): Obtain dl (Version 1)
get_selectivity_v1(): Compute Selectivity-at-Age Across Years
get_aerial_survey_like_v1(): Calculate Aerial Survey Likelihood (Version 1)
get_age_like_v1(): Calculate Age-Frequency Likelihood (Version 1)
get_cpue_like_v1(): Calculate CPUE Likelihood (Version 1)
get_GT_like_v1(): Calculate Gene Tagging (GT) Likelihood (Version 1)
get_harvest_rate_v1(): Calculate Harvest Rate (Version 1)
get_HSP_like_v1(): Calculate Half-Sibling Pair (HSP) Likelihood (Version 1)
get_initial_numbers_v1(): Calculate Initial Numbers-at-Age (Version 1)
get_length_like_v1(): Calculate Length-Frequency Likelihood (Version 1)
get_M_v1(): Calculate Natural Mortality-at-Age (Version 1)
get_phi_v1(): Calculate Reproductive Output-at-Age (Version 1)
get_POP_like_v1(): Calculate POP Likelihood (Version 1)
get_recruitment_prior_v1(): Calculate Recruitment Prior (Version 1)
get_recruitment_v1(): Calculate Recruitment (Version 1)
get_rho_v1(): Calculate Autocorrelation Coefficient (Version 1)
get_sel_like_v1(): Calculate Selectivity Likelihood/Prior (Version 1)
get_tag_like_v1(): Calculate Tagging Likelihood (Version 1)
get_troll_like_v1(): Calculate Troll Survey Likelihood (Version 1)