Package index • sbt

All functions

GTs: Gene tagging

HSPs: Half sibling pairs

POPs: Parent offspring pairs

POPs_v1: Parent offspring pairs

aerial_cov: Aerial survey covariance

aerial_survey: Aerial survey

age_freq: AFs

catch: Catch

catch_UA: Catch UA

check_bounds(): Check if parameters are up against the bounds

check_estimability(): Check for identifiability of fixed effects

cmb(): Helper to make closure

cpue: CPUE

data_csv1: Tables read in from csv files

data_labrep1: Outputs from a single model run

data_par1: Parameter values from a single model run

do_dynamics(): Population dynamics

evaluate_priors(): Evaluate priors

extract_fixed(): Extract fixed effects

get_GT_like(): Genetic tagging likelihood

get_HSP_like(): Half-Sibling Pair Likelihood

get_M(): Natural mortality-at-age

get_M_length(): Natural mortality at age

get_POP_like(): Parent-Offspring Pairing Likelihood

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(): Set up the data input file

get_data_v1(): Set up the data input file

get_dl(): Obtain dl

get_grid(): Set up a grid

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_mcmc_profile(): Run the dynamics

get_parameters(): Get default initial parameter values

get_phi(): Spawning output-at-age

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_sel_list(): Get list of selectivity parameters

get_selectivity(): Compute selectivity-at-age by year

get_selectivity_prior(): Selectivity prior

get_selectivity_v1(): Compute Selectivity-at-Age Across Years

get_sliced_afs(): Obtain the sliced AFs

get_tag_like(): Tag Recapture Likelihood

get_troll_like(): Troll CPUE likelihood

get_weight_at_age(): Obtain the mean weight at age

length_freq: Proportion at length in the catch

length_mean: Mean length at age

length_sd: Standard deviation of mean length at age

paly: Distribution of age given length in genotyped adults

plot_aerial_survey(): Plot aerial survey

plot_af(): Plot AF

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

plot_recruitment(): Plot recruitment

plot_selectivity(): Plot selectivity

plot_sliced_afs(): Plot sliced AFs

plot_tags(): Plot tags

plot_weight_at_age(): Plot weight at age

posfun(): Positive Constraint Penalty Function

project_recruitment(): Project recruitment deviates

project_selectivity(): Project recruitment deviates

rerun_grid(): Run a grid again

run_grid(): Run a grid

sbt_globals(): The globals

sbt_model(): The sbt model

sbt_model_v1(): The sbt model

sbtprofile(): Adaptive likelihood profiling

tag_recaptures: Tag recapture observations

tag_releases: Tag release observations

tag_reporting: Tag reporting rates

troll: Troll