Package index • SPoRC

All functions

Do_Population_Projection(): Do Population Projections

Get_Feedback_Data(): Helper function that obtains data for a simulation with a feedback loop

Get_Reference_Points(): Wrapper function to get reference points

Setup_Mod_Biologicals(): Setup biological inputs for estimation model

Setup_Mod_Catch_and_F(): Setup fishing mortality and catch observations

Setup_Mod_Dim(): Set up model dimensions

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_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_Weighting(): Set up SPoRC model weighting

Setup_Sim_Biologicals(): Set up simulation stuff for biologicals

Setup_Sim_Containers(): Setup containers for simulation and output into global environment

Setup_Sim_Dim(): Set up simulation dimensions

Setup_Sim_FishMort(): Setup values and dimensions of fishing mortality

Setup_Sim_FishSel(): Setup fishery selectivity

Setup_Sim_Observation_Proc(): Set up simulation observation 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_env(): Constructs simulation objects in a new simulation environment for use in simulation functions

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

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

check_data_dimensions(): Helper function used to check data dimensions to ensure they are correct

do_francis_reweighting(): Run Francis Reweighting

do_jitter(): Run Jitter Analysis

do_likelihood_profile(): Run Likelihood Profile

do_mcmc(): Run MCMC using rtmbstan

do_retrospective(): Functino to run retrospective analyses

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

fit_model(): Run RTMB model

get_biological_plot(): Get Plots of Biological Quantities

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

get_data_fitted_plot(): Get Data Fitted to Plot

get_idx_fits(): Gets index fits results

get_idx_fits_plot(): Get Index Fits Plot

get_key_quants(): Generate Key Projection Quantities and Table Plot

get_mcmc_ssb_rec(): Derive SSB and Recruitment from MCMC using posterior samples

get_nLL_plot(): Get plot of negative log likelihood values

get_osa(): Function to format comp data and get OSA residuals from afscOSA (uses afscOSA and compresid as backend to get OSA residuals)

get_retrospective_plot(): Get Retrospective Plot

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

get_selex_plot(): Get Fishery and Survey Selectivity Plots

get_ts_plot(): Get Time Series Plots

mcmc_diag(): Model diagnostics for MCMC

mcmc_par_names(): Gets parameter names from mcmc object

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

mlt_rg_sable_rep: Sablefish report for 5 region case study

plot_all_basic(): Plotting function for all basic quantities

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.

post_optim_sanity_checks(): Post Optimization Model Convergence Checks

run_annual_cycle(): Run Annual Cycle in Simulation Environment

sgl_rg_ebswp_data: EBS Walleye Pollock data for single region case study

sgl_rg_sable_data: Sablefish data for single region case study

sgl_rg_sable_rep: Sablefish report for single region case study

theme_sablefish(): ggplot theme for sablefish

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