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