Model Dimensions

afscOM is an age-structured, multi-sex, multi-fleet, spatially-explicit population dynamics model. The model has been designed to handle any number of age-classes, up to 2 sexes, any number of fishing fleets, and any number of spatial regions, so long as the model parameters are appropriately dimensioned. To parameterize an OM using this package, the following model dimensions should be defined:

  1. nyears: the number of years over which the user intends to run the model for
  2. nages: the number of age classes in the population
  3. nsexes: the number of sexes to model (1 = females only, 2 = females and males)
  4. nregions: the number of spatial regions in the model
  5. nfleets: the number of fishing fleets to simulate catch from (this is the number of fleets that contribute to removals)

If users wish to generate observations from scientific surveys, an additional model dimension must also be defined:

  1. nsurveys: the number of survey fleets to simulate observations from (removals will not be associated with these fleets)

The model is not sensitive to what true age corresponds to the initial age class, so there is no difference between starting a model at, for example, age-2, and starting a model at age-0, so long as recruitment is appropriately scaled.

Throughout the documentation for this package, model dimensions will be routinely referred to in the following format: [nyears, nages, nsexes, nregions, nfleets].

For example, a model of a population of female fish, with 50 age classes, spread across 3 spatial regions, fished by 4 fishing fleets over 100 years, would have model dimensions: [100, 50, 1, 3, 4]