General structure

Inputs

The package relies on reading in excel files different standard fishery dependent/indepedent data and bioenergetics/diet data on each sheet (the first sheet is documentation). I've attached the single species Bering model excel file that has the data for Cod, Pollock, and Arrowtooth together data(BS2017SS). The "write_data" function on line 27 of the BSAI example outputs that as well because the 2016 data are saved internally in the package.

Parameterization

For parameterizing the population and observation model in terms of predation (on/off/functional form), sexes, ages, years, minage, maxage, selectivity, catchability, etc I rely on switches in the control and fleet_control sheets of the excel files and the fit_mod function in the package and default initial values in the build_params function. The first sheet in the excel file should have up to date documentation of the switches. You can also do ?fit_mod in R and it will give you a description of the switches/function.