MSEtool

MSEtool is the core package in the openMSE collection of R packages for fisheries management strategy evaluation (MSE). It provides a complete framework for building operating models, simulating fishery dynamics, and testing the performance of alternative management procedures using closed-loop simulation.

Key Features

• Modular operating model structure: stock biology, fleet dynamics, observation error, and implementation error are each defined as independent S4 objects, making it easy to mix, match, and reuse components across operating models
• Stochastic simulation: all parameters support uncertainty through distributions and inter-annual variability, propagated across user-defined simulation replicates
• Multi-stock and multi-fleet support: operating models can represent complex fishery systems with multiple interacting stocks and fleets, including spatial structure and seasonal dynamics
• Flexible management advice: management procedures can return any combination of output controls, input controls, spatial controls, and gear regulations
• User-defined management procedures: MPs are plain R functions that accept a data object and return an advice object
• Real and simulated data: operating models can be conditioned on real fishery data, and the same data object structure is used for both observed and simulated data. MPs developed and tested in MSE work directly in applied management
• Import from stock assessments: populate operating models directly from stock assessment output (e.g., Stock Synthesis 3 (SS3) & Beaufort Assessment Model (BAM))
• Closed-loop MSE: management procedures are applied to simulated fishery data, with the resulting advice fed back into the population dynamics each year over a multi-year projection period
• Slick integration: export MSE results to Slick for interactive exploration of management procedure performance across operating models and performance metrics

Installation

Install the released version from CRAN:

install.packages("MSEtool")

Or the development version from GitHub:

# install.packages("pak")
# pak::pak("Blue-Matter/MSEtool")
install.packages("MSEtool", repos = c('https://blue-matter.r-universe.dev', 'https://cloud.r-project.org'))

Documentation

• openMSE.com: general information about the openMSE framework
• docs.openMSE.com: technical manual with worked examples covering operating model construction, simulation, and MSE analysis
• msetool.openmse.com: full function reference for MSEtool