Abstract
Simulation testing is an important approach to evaluating fishery stock assessment methods. In the last decade, the fisheries stock assessment modeling framework Stock Synthesis (SS3) has become widely used around the world. However, there lacks a generalized and scriptable framework for SS3 simulation testing. Here, we introduce ss3sim, an R package that facilitates reproducible, flexible, and rapid end-to-end simulation testing with SS3. ss3sim requires an existing SS3 model configuration along with plain-text control files describing alternative population dynamics, fishery properties, sampling scenarios, and assessment approaches. ss3sim then generates an underlying ‘truth’ from a specified operating model, samples from that truth, modifies and runs an estimation model, and synthesizes the results. The simulations can be run in parallel, reducing runtime, and the source code is free to be modified under an open-source MIT license. ss3sim is designed to explore structural differences between the underlying truth and assumptions of an estimation model, or between multiple estimation model configurations. For example, ss3sim can be used to answer questions about model misspecification, retrospective patterns, and the relative importance of different types of fisheries data. We demonstrate the software with an example, discuss how ss3sim complements other simulation software, and outline specific research questions that ss3sim could address.
Highlights
Fisheries stock assessment models are an invaluable tool for providing scientific advice regarding stock status, historical productivity, and changes in stock composition as well as evaluating the impact of alternative management actions on fishery resources [1,2]
A variety of stock assessment approaches are available, it is often not straightforward to select among competing alternatives that may lead to different conclusions about stock status and associated scientific advice to management
Flexible: ss3sim inherits the flexibility of SS3 and can implement many available stock assessment configurations by either modifying existing SS3 model configurations or by modifying generic life-history model configurations that are built into ss3sim (Text S1)
Summary
Fisheries stock assessment models are an invaluable tool for providing scientific advice regarding stock status, historical productivity, and changes in stock composition as well as evaluating the impact of alternative management actions on fishery resources [1,2]. Owing in part to these advantages, SS3 has been used worldwide to formally assess 61 fishery stocks by 2012:35 stocks in the US, 10 tuna/billfish stocks in three oceans, four European stocks, and 12 Australian stocks [17]. These assessments are conducted by both national agencies (e.g. NOAA in the United States of America, CSIRO in Australia) as well as regional fisheries management organizations (e.g. IATTC, ICCAT, IOTC in the Pacific, Atlantic and Indian oceans respectively). In addition to completed formal stock assessments, exploratory SS3 applications for many other stocks are underway [17]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
