Todo list

[PaulRegular]

• Add function for simulating a stratified random survey (sim_sets)
• Add function for simulating complete catch (sim_catch; include growth function here to generate lengths)
• Add sampling functions (set catch, lengths measured, otoliths aged) (sim_samp)
• Add stratified analysis function to obtain strat estimates from simulated survey data
• Add function for testing different survey sampling scenarios
• Use foreach (parallel loop) to speed up test_surveys function
• Profile code to look for efficiencies
• Make a surveys function and modify test_surveys to take the object as an input (vs test_surveys building the grid of surveys internally)
• Enable saving of RData or csv in test_surveys function and add a resume argument
• Add plots of survey sampling to vis_sim flexdashboard
• Calculate intra-haul correlation on real and simulated data (i.e. ICC)
• For the test_survey function, consider using data.table::fwrite and save each survey result in a .csv versus current base::save strategy
• Retain sample size info in survey statistics tables
• Replace current estimate plot with fancharts in vis_sim flexdashboard
• Colour code sets where length cap was reached
• Try and figure out a visual for showing if age cap was reached
• Test survey scenarios on a 'cod' population with decreased patchiness and / or a population tailored to other species
• Write a description of the age-year-space covariance process used in the sim_distribution function
• Add function for calculating effective sample size
• Consider alternates to the RMSE metric that better represents fits to the tails of the population (e.g. log-based metric suggested by Geoff)