Package index • SPoRC

Model Setup

Functions for setting up a SPoRC model

Setup_Mod_Biologicals(): Setup biological inputs for estimation model

Setup_Mod_Catch_and_F(): Setup fishing mortality and catch observations

Setup_Mod_FishIdx_and_Comps(): Setup observed fishery indices and composition data (age and length comps)

Setup_Mod_Fishsel_and_Q(): Setup fishery selectivity and catchability specifications

Setup_Mod_Movement(): Setup Movement Processes for SPoRC

Setup_Mod_Weighting(): Set up SPoRC model weighting

Setup_Mod_Rec(): Setup model objects for specifying recruitment module and associated processes

Setup_Mod_SrvIdx_and_Comps(): Setup observed survey indices and composition data (age and length comps)

Setup_Mod_Srvsel_and_Q(): Setup survey selectivity and catchability specifications

Setup_Mod_Tagging(): Setup tagging processes and parameters

Setup_Mod_Dim(): Set up model dimensions

Reference Points and Projections

Functions for deriving reference points and catch projections

Do_Population_Projection(): Do Population Projections

Get_Reference_Points(): Wrapper function to get reference points

get_key_quants(): Generate Key Projection Quantities and Table Plot

Simulation Setup

Functions for setting up simulations

Setup_Sim_Biologicals(): Set up simulation containers and inputs for biological parameters

Setup_Sim_Containers(): Setup containers for simulation and output

Setup_Sim_Fishing(): Setup values and dimensions of fishing processes

Setup_Sim_Rec(): Set up recruitment dynamics for simulation

Setup_Sim_Survey(): Setup values for survey parameterization

Setup_Sim_Tagging(): Set up simulated tagging dynamics

Setup_Sim_Dim(): Initialize Simulation Dimension Settings

Setup_sim_env(): Constructs simulation objects in a new simulation environment for use in simulation functions

run_annual_cycle(): Run Annual Cycle in Simulation Environment

Simulate_Pop_Static(): Simulates a static spatial, sex, and age-structured population (no feedback loop)

simulation_self_test(): Conduct a Simulation Self Test

simulation_data_to_SPoRC(): Extract simulation data into SPoRC format

Closed-Loop Simulation

Functions for setting up and running closed-loop population simulations

condition_closed_loop_simulations(): Set up simulation list for closed-loop projections

get_closed_loop_reference_points(): Get Closed Loop Reference Points

bisection_F(): Go from TAC to Fishing Mortality using bisection

Francis Reweighting

Functions for setting up Francis Reweighting

run_francis(): Run Iterative Francis Reweighting Procedure

do_francis_reweighting(): Get Francis Weights

Model Diagnostics

Functions for model diagnostics

do_jitter(): Run Jitter Analysis

do_retrospective(): Run retrospective analyses for RTMB models

get_retrospective_relative_difference(): Derive relative difference from terminal year from a retrospective analysis.

do_runs_test(): Runs test function taken from SS3 diags.

get_idx_fits(): Gets index fits results

get_comp_prop(): Gets composition data proportions normalized according to the assessment specifications from RTMB

get_osa(): Compute OSA residuals for composition data

plot_resids(): Plots OSA residuals from outputs from get_osa. Much of this code is taken from the afscOM package, but with modificaitons to plot features.

get_nLL_plot(): Get plot of negative log likelihood values

get_idx_fits_plot(): Get Index Fits Plot

get_catch_fits_plot(): Title Get Catch Fits Plot

get_retrospective_plot(): Get Retrospective Plot

do_likelihood_profile(): Run Likelihood Profile

get_model_rep_from_mcmc(): Extract model report from MCMC posterior samples

Utility

Functions for convenience

fit_model(): Run RTMB model

set_data_indicator_unused(): Set Data Indicators to Unused for Specified Years

post_optim_sanity_checks(): Post Optimization Model Convergence Checks

get_par_est_info(): Helper function for extracting parameter information and names from TMB

rho_trans(): Title Constrains value between -1 and 1

get_logistN_Sigma(): Construct logistic-normal covariance matrix

Plotting

Functions for plotting

get_ts_plot(): Get Time Series Plots

get_selex_plot(): Get Fishery and Survey Selectivity Plots

get_biological_plot(): Get Plots of Biological Quantities

get_data_fitted_plot(): Get Data Fitted to Plot

plot_all_basic(): Plotting function for all basic quantities

theme_sablefish(): ggplot theme for sablefish

Data

Data objects provided by SPoRC

sgl_rg_sable_data: Sablefish data for single region case study

mlt_rg_sable_data: Sablefish data for multi region (5 area) case study

sgl_rg_ebswp_data: EBS Walleye Pollock data for single region case study

three_rg_sable_data: Sablefish data for multi region (3 area) case study

sgl_rg_sable_rep: Sablefish report for single region case study

mlt_rg_sable_rep: Sablefish report for 5 region case study

sgl_rg_dusky_data: Dusky data for single region assessment case study

dusky_rtmb_model: Dusky model outputs from single regino model