General structure - grantdadams/Rceattle GitHub Wiki

Inputs

The package relies on list of data.frames and vectors describing the data and model switches. Data can be stored/created as a list from scratch, from an excel file read in using read_data, or from data-sets included in the package. Examples include the single species Bering model that has the data for Cod, Pollock, and Arrowtooth together in data(BS2017SS). The write_data function will write those data to an excel file with associated meta data.

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.