openMSE Technical Manual

Management Strategy Evaluation with openMSE

Author

Adrian Hordyk, Quang Huynh, and Tom Carruthers

Published

December 9, 2025

Introduction

Welcome to the openMSE Technical Manual.

This book is intended for fisheries scientists and other analysts who wish to learn how to use openMSE for all aspects of Management Strategy Evaluation (MSE):

  • building operating models;
  • developing management procedures;
  • conducting closed-loop simulation testing;
  • summarizing and presenting results.

About openMSE

openMSE is an umbrella R package for building operating models, analyzing fishery data, and conducting Management Strategy Evaluation (MSE) for a wide range of fisheries.

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

For more general information about openMSE see the openMSE website.

Assumed Knowledge

Little programming experience is required to use the openMSE. However, users of the openMSE packages should have some familiarity with R, and be comfortable with using the command line. The technical documentation attempts to explain the use of the openMSE functions and features in easy to follow steps, but familiarity with the most common R functions is assumed.

Installing openMSE

Warning

This Technical Manual has been developed for openMSE 2.0, which is currently under development and has not yet been released on CRAN.

The code in this manual is only compatible with the latest development branches of MSEtool, SAMtool, DLMtool, and openMSE.

This warning will be removed once the openMSE 2.0 packages have been released on CRAN.

The openMSE package is available on CRAN can be installed with:

install.packages('openMSE')

and loaded into the R session with:

Installing and loading the openMSE package will install and load the following core packages:

  1. MSEtool - the Management Strategy Evaluation toolkit is the core package in the openMSE collection. It contains the core functions for constructing operating models, simulating fishery dynamics, and evaluating the effectiveness of alternative management strategies using closed-loop simulation testing.

  2. DLMtool - the Data-Limited Methods toolkit is a collection of data-limited management procedures that can be evaluated using MSE. DLMtool requires the MSEtool package as a dependency, and all MSEtool functions will be available when DLMtool is loaded into an R session.

  3. SAMtool - the Stock Assessment Methods toolkit is a collection of assessment methods and management procedures that have been developed for more data-intensive applications. SAMtool requires the MSEtool package as a dependency, and all MSEtool functions will be available when SAMtool is loaded into an R session.

Important

Currently the latest development version of MSEtool needs to be installed from Github:

pak::pkg_install('blue-matter/MSEtool@prerelease')

Acknowledgements

openMSE development has been made possible through the generous support of the following funders:

We thank The Ocean Foundation for their support of the code refactoring and the development of openMSE 2.0 and this openMSE Technical Manual.

Finally, openMSE is a collaborative effort and we thank all collaborators who have notified us of bugs, provided suggestions for improvement, and helped in countless other ways in continuing the development of the openMSE R packages.