Function reference • sbt

Helper functions

Build a data set or extract something.

get_array(): Convert a 2D array of vectors to an array

get_bounds(): Get default parameter bounds

get_data(): Set up the data input file

get_data_old(): Set up the data input file

get_dl(): Obtain dl

get_grid(): Set up a grid

get_length_at_age(): Obtain the length at age array

get_loo(): Obtain the leave-one-out information criterion (LOO IC)

get_map(): Get default parameter mapping

get_parameters(): Get default initial parameter values

get_posterior(): Obtain samples from the posterior distribution of reported quantities

get_posterior2(): Obtain samples from the posterior distribution of reported quantities

get_sel_list(): Get list of selectivity parameters

get_sliced_afs(): Obtain the sliced AFs

get_weight_at_age(): Obtain the mean weight at age

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

run_grid(): Run a grid

Plots

Plot an input or output.

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_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_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

Data

Example data sets and outputs from the ADMB model.

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

cpue: CPUE

aerial_survey: Aerial survey

aerial_cov: Aerial survey covariance

troll: Troll

catch: Catch

catch_UA: Catch UA

POPs: Parent offspring pairs

POPsv2: Parent offspring pairs

paly: Distribution of age given length in genotyped adults

HSPs: Half sibling pairs

GTs: Gene tagging

age_freq: AFs

length_freq: Proportion at length in the catch

length_mean: Mean length at age

length_sd: Standard deviation of mean length at age

tag_recaptures: Tag recapture observations

tag_releases: Tag release observations

tag_reporting: Tag reporting rates

cpp1: Copy of version 1 code

hpp1: Copy of version 1 code