Package index • opal

All functions

bet_globals(): The globals
check_bounds(): Check if parameters are up against the bounds
check_estimability(): Check for identifiability of fixed effects
check_grid(): Check estimability of the grid
cmb(): Helper to make closure
convert_rtmb_selex_to_ss3(): Convert RTMB real-line selectivity parameters back to SS3 natural scale
convert_ss3_selex_to_rtmb(): Convert SS3 selectivity parameters to RTMB real-line parameterization
do_dynamics(): Population dynamics
evaluate_priors(): Evaluate priors
extract_fixed(): Extract fixed effects
get_M(): Natural mortality at age
get_M_length(): Natural mortality at length
get_bounds(): Get default parameter bounds
get_cor_pairs(): Return strongly-correlated parameter pairs
get_cpue_like(): CPUE index likelihood
get_data(): Set up the data input file
get_dl(): Obtain dl
get_grid(): Set up a grid
get_growth(): Compute mean length-at-age using the Schnute parameterization of VB growth
get_harvest_rate(): Harvest rate calculation
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_map(): Get default parameter mapping
get_maturity_at_age(): Convert maturity-at-length to maturity-at-age
get_mcmc_profile(): Run the dynamics
get_par_table(): Summarise model parameters in a table
get_parameters(): Get default initial parameter values
get_pla(): Probability of length at age matrix (age-length key)
get_posterior(): Obtain samples from the posterior distribution of reported quantities
get_posterior2(): Obtain samples from the posterior distribution of reported quantities
get_posterior3(): 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_sd_at_age(): Compute SD of length-at-age from CV1 and CV2
get_selectivity(): Compute selectivity-at-age from length-based selectivity curves
get_weight_at_age(): Obtain the mean weight at age
get_weight_at_length(): Compute weight at each length bin midpoint
get_weight_like(): Weight Composition Likelihood
grid_to_snutsfit(): Convert grid to an snutsfit object
opal_baseline: opal model regression baseline
opal_baseline_data: Opal Baseline Data
opal_baseline_map: Opal Baseline Map
opal_baseline_parameters: Opal Baseline Parameters
opal_model(): The opal model
opalprofile(): Adaptive likelihood profiling
plot_af(): Plot age frequency
plot_biomass_spawning(): Plot spawning biomass
plot_catch(): Plot catch
plot_cpue(): Plot CPUE
plot_cpue_lf(): Plot LF
plot_dist_length_at_age(): Plot the distribution of length at age
plot_hrate(): Plot harvest rate
plot_initial_numbers(): Plot initial numbers
plot_length_at_age(): Plot length at age
plot_lf(): Plot LF
plot_loo(): Plot PSIS LOO
plot_natural_mortality(): Plot natural mortality
plot_profile(): Run the dynamics
plot_rec_devs(): Plot recruitment deviates
plot_recruitment(): Plot recruitment
plot_selectivity(): Plot selectivity
plot_weight_at_age(): Plot weight at age
posfun(): Positive Constraint Penalty Function
prep_lf_data(): Prepare length composition data for model input
prep_wf_data(): Prepare weight composition data for model input
project_dynamics(): Project dynamics
project_rec_devs(): Project recruitment deviates
project_selectivity(): Project recruitment deviates
rebin_counts(): Linear area rebinning of frequency data
rebin_matrix(): Compute rebinning weight matrix
rerun_grid(): Run a grid again
resolve_bio_vector(): Resolve a biology vector to age-basis
run_grid(): Run a grid
sample_grid(): Sample from the grid
sel_double_normal(): Double-normal selectivity as a function of length (SS3 pattern 24, full form)
sel_logistic(): Logistic selectivity as a function of length
wcpo_bet_data: West Central Pacific Ocean Bigeye Tuna (WCPO BET) Assessment Data
wcpo_bet_lf: West Central Pacific Ocean Bigeye Tuna (WCPO BET) Length Frequency Data
wcpo_bet_parameters: West Central Pacific Ocean Bigeye Tuna (WCPO BET) Assessment Parameters
wcpo_bet_wf: West Central Pacific Ocean Bigeye Tuna (WCPO BET) Weight Frequency Data