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mizerEcopath

Gustav Delius

Source: vignettes/mizerEcopath.qmd

Introduction

This package provides functions that help to create a mizer model based on the parameters of an Ecopath model.

I still have to write the instructions, but the general procedure is as follows:

  1. You open the Ecopath model in Ecopath with Ecosim and export the parameters to a CSV file. (Details to follow)

  2. You load these files into R.

  3. You create a table with one row for each species you want to include in the mizer model. The table must contain the following columns:

  • species: The name of the species in the mizer model
  • w_max: The largest observed size of the species
  • w_mat: The weight at maturity of the species
  • ecopath_groups: The Ecopath group corresponding to this species. If in the Ecopath model the species is split into several stanzas, then this column should contain a vector of the names of the stanzas that need to be combined to give the values for this species.

  1. You pass this table and the Ecopath tables to the newAllometricParams() to create a mizer model based on these parameters.

  2. You load in information on the size-structure of the fishery catches.

  3. You use the shiny gadget tuneEcopath() to fine-tune the mizer model to reproduce the observed size structure.

  4. You turn on the dynamics and run the model.