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ss3sim: an R package for fisheries Stock Assessment simulation with stock synthesis.

Anderson SC, Monnahan CC, Johnson KF, Ono K, Valero JL - PLoS ONE (2014)

Bottom Line: 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.We demonstrate the software with an example, discuss how ss3sim complements other simulation software, and outline specific research questions that ss3sim could address.

View Article: PubMed Central - PubMed

Affiliation: Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.

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.

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Flow diagram of the main steps in an ss3sim simulation carried out using run_ss3sim.Functions that are called internally are shown in a monospaced font.
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pone-0092725-g001: Flow diagram of the main steps in an ss3sim simulation carried out using run_ss3sim.Functions that are called internally are shown in a monospaced font.

Mentions: ss3sim consists of both low-level functions that modify SS3 configuration files and high-level functions that combine these low-level functions into a complete simulation experiment (Figure 1, Table 1). In this paper we will focus on the structure and use of the high-level function run_ss3sim; however, the low-level functions can be used on their own as part of a customized simulation (see the R package vignette at http://cran.r-project.org/package=ss3sim).


ss3sim: an R package for fisheries Stock Assessment simulation with stock synthesis.

Anderson SC, Monnahan CC, Johnson KF, Ono K, Valero JL - PLoS ONE (2014)

Flow diagram of the main steps in an ss3sim simulation carried out using run_ss3sim.Functions that are called internally are shown in a monospaced font.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3974719&req=5

pone-0092725-g001: Flow diagram of the main steps in an ss3sim simulation carried out using run_ss3sim.Functions that are called internally are shown in a monospaced font.
Mentions: ss3sim consists of both low-level functions that modify SS3 configuration files and high-level functions that combine these low-level functions into a complete simulation experiment (Figure 1, Table 1). In this paper we will focus on the structure and use of the high-level function run_ss3sim; however, the low-level functions can be used on their own as part of a customized simulation (see the R package vignette at http://cran.r-project.org/package=ss3sim).

Bottom Line: 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.We demonstrate the software with an example, discuss how ss3sim complements other simulation software, and outline specific research questions that ss3sim could address.

View Article: PubMed Central - PubMed

Affiliation: Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.

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.

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