1 What is FishSimGTG?

FishSimGTG is an R package that conducts numerical modeling of fish populations, including management strategy evaluation (MSE) and is an age-structured model that represents multiple concurrent cohorts using the growth-type-group methodology (Walters and Martell 2004). This framework is typically used to quantify trade-offs among competing management strategies or management options in terms of expected achievement of fishery management objectives. These trade-offs emerge from modeling results that are obtained from analysis methods like management strategy evaluation (MSE) or population dynamics projection. Calculation of trade-offs can play a meaningful role in supporting the development fishery management plans and fishery rule making. Simulations are implemented in the R statistical computing environment (R Core Team 2022). This framework is not a ‘black box’ software, and thus, it is intended to be customized to address specific questions related to fishery management.

1.1 Installation and required packages

FishSimGTG is coded in R (R Core Team 2022) and requires some basic packages that can be installed as follows:

  1. Install R:

    • Go to the CRAN website.
    • Download and install the appropriate version of R for your operating system (Windows, macOS, or Linux).

  2. Install RStudio:

    • Go to the RStudio website.
    • Download and install RStudio Desktop (free version).

  3. Installing Required Packages:

The user can install the necessary packages to run the simulation and visualize the outputs by using the following R commands:

install.packages("devtools")
library(devtools)

devtools::install_github("natureanalytics-ca/fishSimGTG")
devtools::install_github("natureanalytics-ca/fishSimTools")
  1. Load the Required Packages:
library(fishSimGTG)
library(fishSimTools)

The core packages required to run the simulation are fishSimGTG and fishSimTools. The devtools package is necessary because it allows us to install these core packages directly from GitHub, ensuring we have the latest versions and updates.

1.2 How to use FishSimGTG?

The FishSimGTG package can be used to construct an operating model (OM) that simulates population and fishery dynamics, including data collection and the application of user-customized management procedures. The OM consists of several S4-type objects, such as the LifeHistory object, Fishery object, and TimeArea object, etc. These objects store parameters and information in slots, which users can access using the @ symbol.

This user guide provides a full description of the S4 object components and instructions on how to populate each object to create the OM.

References

R Core Team. 2022. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Walters, Carl J, and Steven JD Martell. 2004. Fisheries Ecology and Management. Princeton University Press.