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 relationships with covariates

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