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")

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. Load the Required Packages:
library(fishSimGTG)
library(fishSimTools)

The core packages required to run the simulation are fishSimGTG and fishSimTools. ## 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.