Package index • SPoRC

Model Setup

Functions for setting up a SPoRC model

Setup_Mod_Biologicals(): Set up biological inputs for the estimation model
Setup_Mod_Catch_and_F(): Set up fishing mortality, discard mortality, and catch observation inputs
Setup_Mod_FishIdx_and_Comps(): Set up discards, fishery index, age composition, and length composition inputs
Setup_Mod_Fishsel_and_Q(): Set up total and retained fishery selectivity and catchability specifications
Setup_Mod_Movement(): Set up movement model inputs and parameter structures
Setup_Mod_Weighting(): Set likelihood and penalty weights for the estimation model
Setup_Mod_Rec(): Set up the recruitment module and associated processes
Setup_Mod_SrvIdx_and_Comps(): Set up observed survey indices and composition data
Setup_Mod_Srvsel_and_Q(): Set up survey selectivity and catchability specifications
Setup_Mod_Tagging(): Set up the conventional tagging module for model fitting
Setup_Mod_Dim(): Initialise model dimension settings

Functions for deriving reference points and catch projections

Do_Population_Projection(): Do Population Projections
Get_Reference_Points(): Compute fishing and biological reference points from an assessment or simulation
get_key_quants(): Generate Key Projection Quantities and Table Plot

Functions for setting up simulations

Setup_Sim_Biologicals(): Set up biological parameter inputs for closed-loop simulation
Setup_Sim_Containers(): Initialise output containers for the operating model simulation
Setup_Sim_Fishing(): Setup Simulation Fishing Inputs
Setup_Sim_Rec(): Set up recruitment dynamics for the operating model simulation
Setup_Sim_Survey(): Set up survey parameterisation for the operating model simulation
Setup_Sim_Tagging(): Set up conventional tagging dynamics for the operating model simulation
Setup_Sim_Dim(): Initialise simulation dimension settings
Setup_sim_env(): Construct and populate a simulation execution environment
run_annual_cycle(): Run the annual cycle for a single simulation year
Simulate_Pop_Static(): Simulate a static (open-loop) spatial age- and sex-structured population
simulation_self_test(): Run a simulation self-test of a fitted RTMB estimation model
simulation_data_to_SPoRC(): Extract simulation outputs into SPoRC estimation model format

Functions for setting up and running closed-loop population simulations

condition_closed_loop_simulations(): Construct and Condition Closed-Loop Simulation Inputs
get_closed_loop_reference_points(): Get Closed Loop Reference Points
catch_to_F_singlefleet(): Convert a target catch to fishing mortality for a single fleet via bisection
catch_to_F_multifleet(): Convert target catches to fishing mortality rates for multiple fleets

Functions for setting up Francis Reweighting

Functions for model diagnostics

do_jitter(): Run Jitter Analysis for Model Diagnostics
do_retrospective(): Run Retrospective Diagnostics for RTMB Models
get_retrospective_relative_difference(): Derive relative difference from terminal year from a retrospective analysis.
do_runs_test(): Runs Test for Residual Randomness
get_idx_fits(): Extract Index Fit Results
get_comp_prop(): Get Composition Proportions from RTMB Output
get_osa(): Compute OSA residuals for composition data
plot_resids(): Plot OSA residuals from outputs of get_osa
get_nLL_plot(): Get Plot of Negative Log Likelihood Values
get_idx_fits_plot(): Get Index Fits Plot
get_catch_fits_plot(): Get Catch and Discard Fits Plot
get_retrospective_plot(): Get Retrospective Plot
do_likelihood_profile(): Run Likelihood Profile
get_model_rep_from_mcmc(): Extract model report quantities from MCMC posterior samples
marg_AIC(): Compute the corrected marginal AIC (AICc)

Functions for convenience

fit_model(): Fit a SPoRC RTMB model
set_data_indicator_unused(): Set data indicators to unused for specified years
post_optim_sanity_checks(): Run post-optimisation convergence checks on a fitted SPoRC model
get_par_est_info(): Extract and tabulate parameter estimates and metadata from a fitted SPoRC model
rho_trans(): Transform a real-valued parameter to the interval (-1, 1)
get_logistN_Sigma(): Construct a logistic-normal covariance matrix

Functions for plotting

Data objects provided by SPoRC