openMSE Technical Manual

Management Strategy Evaluation with openMSE

Author

Adrian Hordyk, Quang Huynh, and Tom Carruthers

Published

July 27, 2026

1 Introduction

openMSE is a framework for building operating models, analyzing fishery data, and conducting Management Strategy Evaluation (MSE).

This manual is intended for fisheries scientists and analysts who wish to use openMSE for all stages of an MSE, including:

  • building and conditioning operating models;
  • simulating historical fishery dynamics;
  • developing and testing management procedures;
  • conducting closed-loop simulation testing;
  • summarizing and presenting results.

1.1 About openMSE

openMSE is an umbrella R package comprising three core packages:

  1. MSEtool: the Management Strategy Evaluation toolkit. The core package in the collection, containing the primary functions for constructing operating models, simulating fishery dynamics, and running closed-loop MSE.

  2. DLMtool: the Data-Limited Methods toolkit. A library of data-limited management procedures for use with MSEtool.

  3. SAMtool: the Stock Assessment Methods toolkit. A library of model-based assessment methods and management procedures for data-intensive applications. Includes the Rapid Conditioning Model.

Loading openMSE into an R session automatically loads all three packages. Each package has its own documentation page (linked above); this manual focuses on the overall framework.

openMSE was developed by Adrian Hordyk, Quang Huynh, and Tom Carruthers at Blue Matter Science.

1.2 Prerequisites

To use openMSE or any of its component packages you must have:

  1. A recent version of the R software installed on your machine;
  2. While not essential, we highly recommend using an integrated development environment (IDE) such as RStudio;
  3. The latest version of openMSE and the individual component packages installed.

1.2.1 Installing R

The R statistical language and environment can be freely downloaded from the CRAN website and is available for all operating systems. Updated versions of R are released frequently, and it is recommended that you have the latest version installed.

Head to the CRAN website to download the latest version of R.

You can check your version of R by typing version into the R console.

1.2.2 Installing RStudio

RStudio is a freely available integrated development environment (IDE) for R. It is not essential that you use RStudio, but it can make things a lot easier, especially if you are new to R.

We assume throughout the openMSE documentation that you are using RStudio.

It is important to be aware that RStudio and R are two different pieces of software that must be installed separately. We recommend installing the R software before downloading and installing RStudio.

1.2.3 Installing openMSE

We recommend installing openMSE using pak, which automatically checks that all dependency packages meet the minimum version requirements:

# Install pak if required
if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak")

# Install openMSE and dependencies
pak::pak("openMSE")

To upgrade all packages to the latest versions:

pak::pak("openMSE", upgrade = TRUE)

Then load openMSE into your R session:

ImportantDevelopment Version

MSEtool v4.0 has not yet been released on CRAN and must be installed from GitHub:

pak::pkg_install("blue-matter/MSEtool")

All code in this manual works with this development version. The existing CRAN versions of openMSE, DLMtool, and SAMtool are compatible. This note will be removed once MSEtool v4.0 is released on CRAN.

1.3 About Version 2.0

openMSE 2.0 is a major update featuring a complete redesign of the core S4 object classes and a full refactoring of the source code. It is backwards compatible; code written for earlier versions should continue to work without modification, though for new work we recommend following the methods described in this manual. For a full description of changes see Appendix B.