Reference

Simulate abundance
sim_abundance()	Simulate basic population dynamics model
sim_R() sim_Z() sim_N0()	Simulate starting abundance, random recruitment and total mortality
sim_vonB()	Closure for simulating length given age using von Bertalanffy notation
Simulate distribution
sim_distribution()	Simulate spatial and temporal distribution
sim_ays_covar()	Simulate age-year-space covariance
sim_ays_covar_spde()	Simulate age-year-space covariance using SPDE approach
sim_parabola()	Define a parabolic relationship
sim_nlf()	Define a non-linear relationship
make_grid()	Make a depth stratified survey grid
make_mesh()	Make an R-INLA mesh based off a grid
Simulate survey
sim_survey()	Simulate stratified-random survey
sim_survey_parallel()	Simulate stratified random surveys using parallel computation
sim_logistic()	Closure for simulating logistic curve
sim_sets()	Simulate survey sets
Stratified analysis
run_strat()	Run stratified analysis on simulated data
strat_error()	Calculate error of stratified estimates
error_stats()	Calculate common error statistics
strat_data()	Prepare simulated data for stratified analysis
strat_means()	Calculate stratified means, variances and confidence intervals across groups
Testing multiple surveys
test_surveys() resume_test()	Test sampling design of multiple surveys using a stratified analysis
expand_surveys()	Set-up a series of surveys from all combinations of settings supplied
Plotting functions
plot_trend() plot_surface() plot_grid() plot_distribution() plot_survey() plot_total_strat_fan() plot_length_strat_fan() plot_age_strat_fan() plot_error_surface() plot_survey_rank()	Simple plotting functions
vis_sim()	Make a flexdashboard for visualizing the simulation
Helpers
round_sim()	Round simulated population
convert_N()	Convert abundance-at-age matrix to abundance-at-length
group_lengths()	Convert length to length group
icc()	Calculate intraclass correlation
fibonacci()	Generate Fibonacci sequence
object_size()	Print object size
Data
bathy	Southern Newfoundland bathymetry
land	Southern Newfoundland coastline
survey_grid	Sample survey simulation grid.
survey_lite_mesh	Lite sample survey mesh and related items
survey_mesh	Sample survey meshes and related items