Package index • sbt

Data

Datasets included in the package.

GTs: Gene tagging
HSPs: Half sibling pairs
POPs: Parent offspring pairs
POPs_v1: Parent offspring pairs (version 1)
aerial_cov: Aerial survey covariance
aerial_survey: Aerial survey
age_freq: Age frequencies
catch: Catch
catch_UA: Catch unaccounted
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
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
tag_recaptures: Tag recapture observations
tag_releases: Tag release observations
tag_reporting: Tag reporting rates
troll: Troll

Plots

Functions for visualising model outputs.

plot_aerial_survey(): Plot aerial survey
plot_af(): Plot age frequency
plot_biomass_spawning(): Plot spawning biomass
plot_catch(): Plot catch
plot_cpue(): Plot CPUE
plot_cpue_lf(): Plot CPUE 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(): Plot likelihood profiles
plot_rec_devs(): Plot recruitment deviates
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

Functions

Functions for model building, fitting, and inference.

GTs: Gene tagging
HSPs: Half sibling pairs
POPs: Parent offspring pairs
POPs_v1: Parent offspring pairs (version 1)
aerial_cov: Aerial survey covariance
aerial_survey: Aerial survey
age_freq: Age frequencies
catch: Catch
catch_UA: Catch unaccounted
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
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
extend_hsp_cohorts(): Extend HSP data set
extract_fixed(): Extract fixed effects
find_msy(): Find MSY
get_GT_like(): Genetic tagging likelihood
get_GT_like_v1(): Calculate Gene Tagging (GT) Likelihood (Version 1)
get_HSP_like(): Half-sibling pair likelihood
get_HSP_like_v1(): Calculate Half-Sibling Pair (HSP) Likelihood (Version 1)
get_M(): Natural mortality at age
get_M_length(): Natural mortality at length
get_M_v1(): Calculate Natural Mortality-at-Age (Version 1)
get_POP_like(): Parent-Offspring Pairing Likelihood
get_POP_like_v1(): Calculate POP Likelihood (Version 1)
get_POP_like_v2(): Calculate POP Likelihood (Version 2)
get_aerial_survey_like(): Aerial survey likelihood
get_aerial_survey_like_v1(): Calculate Aerial Survey Likelihood (Version 1)
get_age_like(): Age composition likelihood
get_age_like_v1(): Calculate Age-Frequency Likelihood (Version 1)
get_bounds(): Get default parameter bounds
get_cpue_length_like(): CPUE length composition likelihood
get_cpue_like(): CPUE index likelihood
get_cpue_like_v1(): Calculate CPUE Likelihood (Version 1)
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_harvest_rate_v1(): Calculate Harvest Rate (Version 1)
get_initial_numbers(): Initial numbers and Beverton-Holt parameters
get_initial_numbers_v1(): Calculate Initial Numbers-at-Age (Version 1)
get_length_at_age(): Obtain the length at age array
get_length_like(): Length Composition Likelihood
get_length_like_v1(): Calculate Length-Frequency Likelihood (Version 1)
get_loo(): Obtain the leave-one-out information criterion (LOO IC)
get_map(): Get default parameter mapping
get_mcmc_profile(): MCMC likelihood profiling
get_parameters(): Get default initial parameter values
get_phi(): Spawning output-at-age
get_phi_v1(): Calculate Reproductive Output-at-Age (Version 1)
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_recruitment_prior_v1(): Calculate Recruitment Prior (Version 1)
get_recruitment_v1(): Calculate Recruitment (Version 1)
get_rho(): Estimate temporal autocorrelation in recruitment deviations
get_rho_v1(): Calculate Autocorrelation Coefficient (Version 1)
get_sel_like_v1(): Calculate Selectivity Likelihood/Prior (Version 1)
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 Sliced Age Frequencies from Length Frequencies
get_tag_like(): Tag Recapture Likelihood
get_tag_like_v1(): Calculate Tagging Likelihood (Version 1)
get_troll_like(): Troll CPUE likelihood
get_troll_like_v1(): Calculate Troll Survey Likelihood (Version 1)
get_weight_at_age(): Obtain the mean weight at age
grid_to_tmbfit(): Convert sampled grid to a tmbfit object
length_freq: Proportion at length in the catch
length_mean: Mean length at age
length_sd: Standard deviation of mean length at age
load_grid(): Load a grid of MCMCs
msy_calc(): MSY calculation
msy_model(): MSY Calculation Model
paly: Distribution of age given length in genotyped adults
plot_aerial_survey(): Plot aerial survey
plot_af(): Plot age frequency
plot_biomass_spawning(): Plot spawning biomass
plot_catch(): Plot catch
plot_cpue(): Plot CPUE
plot_cpue_lf(): Plot CPUE 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(): Plot likelihood profiles
plot_rec_devs(): Plot recruitment deviates
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_dynamics(): Project dynamics
project_rec_devs(): Project recruitment deviates
project_selectivity(): Project selectivity
rerun_grid(): Run a grid again
run_grid(): Run a grid
sample_grid(): Sample from the grid
save_grid(): Save a grid of MCMCs
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