Todo list #1
Description
- 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)