Technical Manual for the mse FLR/a4a package

Iago MOSQUEIRA (WMR)

Ernesto JARDIM (MSC)

24 November, 2021

Source: vignettes/mse-manual.Rmd

Introduction

This is an introduction.

S4 classes

FLom

**FLom class**: Structure of the FLom class. Slot name followed by the slot class, in parenthesis.

FLom class: Structure of the FLom class. Slot name followed by the slot class, in parenthesis.

FLmse

**FLmse class**: Structure of the FLmse class. Slot name followed by the slot class, in parenthesis.

FLmse class: Structure of the FLmse class. Slot name followed by the slot class, in parenthesis.

FLoem

FLiem

mpCtrl

mseCtrl

Functions

mp()

Workflow of the mp() function.

Workflow of the mp() function.

args

The mp() function takes as input a named list called args. These are arguments of the MSE run, and determine the time frame, frequency of application and lags. Only one argument is required:

  • iy, intermediate year. Only required element in args. The first year in which the procedure is applied.

For all other, default values are generated acording to the om object dimensions, or from internal defaults, as follows:

  • y0, first year. Defaults to start of om.
  • fy, final year. Defaults to last year of om.
  • nsqy, number of years to use for status quo calculations. Defaults to 3.
  • it, number of iterations. Defaults to iterations in om.
  • data_lag, difference between final year of data and iy. Defaults to 1.
  • management_lag, number of years between year of year of application and implementation.
  • frq, frequency. How often is the procedure to be applied, and for how long is a recommendation valid. Defaults to 1.

All these values can be simply overiden by including them in the args argument to mp(). The complete list of arguments is available to every (???) function in any element in the MSE control. In addition, these year dimension nbames vector, generated inside mp(), can also be used in any module function:

  • vy, the years in which the procedure is to be applied, from iy to fy. A character vector.

performance()

Extending mse with your own functions

hcr

sa

More information

  • You can submit bug reports, questions or suggestions on mse at the mse issue page,1 or on the FLR mailing list.
  • Or send a pull request to https://github.com/flr/mse/
  • For more information on the FLR Project for Quantitative Fisheries Science in R, visit the FLR webpage.2
  • The latest version of mse can always be installed using the devtools package, by calling

Software Versions

  • R version 4.1.2 (2021-11-01)
  • FLCore: 2.6.18.9002
  • mse: 2.2.1.9001
  • Compiled: Wed Nov 24 07:45:17 2021
  • Git Hash: ec43547

Author information

Iago MOSQUEIRA. Wageningen Marine Research. Ernesto JARDIM. Marine Stewardship Council.

References

  1. https://github.com/flr/mse/issues↩︎

  2. http://flr-project.org↩︎