Developing a new model

Potential workflow for building a hake cannibalism CEATTLE model I'd suggest the following steps for building the model in Rceattle:

Single species (start here)

1. Use the the BS2017SS excel file (written from code below) as a basis to bridge to the new model.

library(Rceattle) data(BS2017SS) # ?BS2017SS for more information on the data

# Write data to excel Rceattle::write_data(data_list = BS2017SS, file = "BS2017SS.xlsx")

2. Update the control for the specifications of population model

3. Update the fleet_control for the specifications of observation model (surveys/fisheries). This includes parameterizations for catchability/selectivity.

4. Update data on srv_biom, fsh_biom, comp_data

5. If comp_data are length based, update the age_transition matrix (time-invariant currently)

6. If ageing error is present update age_error sheet (time-invariant currently)

7. Update life history bits (wt, pmature, sex_ratio, M1_base sheets for weight(kg), maturity-at-age, proportion female at age, natural/residual mortality at age [can also estimate], respectively)

8. Fit in R and compare to the SS model

Multi-species This may depend on how the bioenergetics and diet data end up looking like!

9. Update the bioenergetic parameterization on the bioenergetics_control and Pyrs (foraging days) sheets

10. Update residual M1 on M1_base sheet if fixed (or can estimate by setting est_M1 != 0)

11. Update bottom/sea-surface temperature on env_data sheet

12. Update diet data. Proportion of prey-at-age by weight in the stomach of a predator at-age on the UobsWtAge sheet

13. Fit in R and celebrate

NOTE: Mn_LatAge and aLW do not need to be updated unless fitting alternative suitability functions. UobsAge is not currently used.