@article{puts_insights_2020b,

title = {Insights on integrating habitat preferences in process-oriented ecological models \textendash a case study of the southern North Sea},

author = {M. P\"{u}ts and M. Taylor and I. N\'{u}\~{n}ez-Riboni and J. Steenbeek and M. St\"{a}bler and C. M\"{o}llmann and A. Kempf},

url = {http://www.sciencedirect.com/science/article/pii/S030438002030260X},

doi = {10.1016/j.ecolmodel.2020.109189},

issn = {0304-3800},

year  = {2020},

date = {2020-09-01},

urldate = {2020-09-01},

journal = {Ecological Modelling},

volume = {431},

pages = {109189},

keywords = {Ecopath with Ecosim, Ecospace, Food web model, Habitat capacity, Spatial-temporal framework, species distribution model},

pubstate = {published},

tppubtype = {article}

}

@article{putsInsightsIntegratingHabitat2020,

title = {Insights on Integrating Habitat Preferences in Process-Oriented Ecological Models \textendash a Case Study of the Southern North Sea},

author = {Miriam P\"{u}ts and Marc Taylor and Ismael N\'{u}\~{n}ez-Riboni and Jeroen Steenbeek and Moritz St\"{a}bler and Christian M\"{o}llmann and Alexander Kempf},

doi = {10.1016/j.ecolmodel.2020.109189},

issn = {0304-3800},

year  = {2020},

date = {2020-09-01},

urldate = {2020-06-30},

journal = {Ecological Modelling},

volume = {431},

pages = {109189},

abstract = {One of the most applied tools to create ecosystem models to support management decisions in the light of ecosystem-based fisheries management is Ecopath with Ecosim (EwE). Recently, its spatial routine Ecospace has evolved due to the addition of the Habitat Foraging Capacity Model (HFCM), a spatial-temporal dynamic niche model to drive the foraging capacity to distribute biomass over model grid cells. The HFCM allows for continuous implementation of externally derived habitat preference maps based on single species distribution models. So far, guidelines are lacking on how to best define habitat preferences for inclusion in process-oriented trophic modeling studies. As one of the first studies, we applied the newest Ecospace development to an existing EwE model of the southern North Sea with the aim to identify which definition of habitat preference leads to the best model fit. Another key aim of our study was to test for the sensitivity of implementing externally derived habitat preference maps within Ecospace to different time-scales (seasonal, yearly, multi-year, and static). For this purpose, generalized additive models (GAM) were fit to scientific survey data using either presence/absence or abundance as differing criteria of habitat preference. Our results show that Ecospace runs using habitat preference maps based on presence/absence data compared best to empirical data. The optimal time-scale for habitat updating differed for biomass and catch, but implementing variable habitats was generally superior to a static habitat representation. Our study hence highlights the importance of a sigmoidal representation of habitat (e.g. presence/absence) and variable habitat preferences (e.g. multi-year) when combining species distribution models with an ecosystem model. It demonstrates that the interpretation of habitat preference can have a major influence on the model fit and outcome.},

keywords = {Ecopath with Ecosim, Ecospace, Food web model, Habitat capacity, Spatial-temporal framework, species distribution model},

pubstate = {published},

tppubtype = {article}

}

@article{pennino_discard_2020,

title = {Discard ban: A simulation-based approach combining hierarchical Bayesian and food web spatial models},

author = {M. Grazia Pennino and A. H. Bevilacqua and M. Angeles Torres and J. M. Bellido and J. Sole and J. Steenbeek and M. Coll},

url = {https://www.sciencedirect.com/science/article/pii/S0308597X18307954},

doi = {10.1016/j.marpol.2019.103703},

issn = {0308-597X},

year  = {2020},

date = {2020-06-01},

urldate = {2020-06-01},

journal = {Marine Policy},

volume = {116},

pages = {103703},

keywords = {Bayesian model, Discards, Ecospace, Food web model, Landing obligation, Mediterranean Sea, spatial ecology},

pubstate = {published},

tppubtype = {article}

}

@article{penninoDiscardBanSimulationbased2020,

title = {Discard Ban: A Simulation-Based Approach Combining Hierarchical Bayesian and Food Web Spatial Models},

author = {Maria Grazia Pennino and Ana Helena Bevilacqua and M. Angeles Torres and Jose M. Bellido and Jordi Sole and Jeroen Steenbeek and Marta Coll},

doi = {10.1016/j.marpol.2019.103703},

issn = {0308-597X},

year  = {2020},

date = {2020-06-01},

urldate = {2021-02-10},

journal = {Marine Policy},

volume = {116},

pages = {103703},

abstract = {Discarding is one of the most important topics in fisheries management, both for economic and ecological reasons. The European Union has included, through the current EU Common Fisheries Policy (CFP) Regulation, a discard ban with a quite controversial instrument: to enforce the landing of unwanted catch as a measure to promote their reduction. This management decision may condition the future of the fishing exploitation in European Sea. Within this context, both stakeholders and policy makers are now claiming for more effective tools that can be used to support the decision-making framework. In this study, we propose a simulation-based approach combining hierarchical Bayesian Spatial Models (H-BSMs) with the spatial-temporal module of Ecopath with Ecosim (EwE) approach, Ecospace, in the North Western Mediterranean Sea. In particular, we firstly assessed high-density discard areas using H-BSMs with fisheries and environmental data, and secondly, we simulated potential management options to identify the trade-offs of the discard ban application within these areas using EwE. We argue that coupling novel methods, as the ones used in this study, could be a decisive step to identify the best management action among a set of different scenarios within the context of the discard ban application in European Seas.},

keywords = {Bayesian model, Discards, Ecospace, Food web model, Landing obligation, Mediterranean Sea, spatial ecology},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeek_ecopath_2016b,

title = {Ecopath with Ecosim as a model-building toolbox: Source code capabilities, extensions, and variations},

author = {J. Steenbeek and J. Buszowski and V. Christensen and E. Akoglu and K. Aydin and N. Ellis and D. Felinto and J. Guitton and S. Lucey and K. Kearney and S. Mackinson and M. Pan and M. Platts and C. J. Walters},

url = {http://www.sciencedirect.com/science/article/pii/S030438001500280X},

doi = {10.1016/j.ecolmodel.2015.06.031},

issn = {0304-3800},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Ecological Modelling},

volume = {319},

pages = {178--189},

keywords = {Ecopath with Ecosim, ecosystem, fisheries, Food web model, model interoperability, Open source software},

pubstate = {published},

tppubtype = {article}

}

@article{steenbeekEcopathEcosimModelbuilding2016,

title = {Ecopath with Ecosim as a Model-Building Toolbox: Source Code Capabilities, Extensions, and Variations},

author = {Jeroen Steenbeek and Joe Buszowski and Villy Christensen and Ekin Akoglu and Kerim Aydin and Nick Ellis and Dalai Felinto and Jerome Guitton and Sean Lucey and Kelly Kearney and Steven Mackinson and Mike Pan and Mark Platts and Carl Walters},

doi = {10.1016/j.ecolmodel.2015.06.031},

issn = {0304-3800},

year  = {2016},

date = {2016-01-01},

urldate = {2015-09-09},

journal = {Ecological Modelling},

volume = {319},

pages = {178\textendash189},

abstract = {Ecopath with Ecosim (EwE) is a widely applied food web model that is mostly known as desktop software for the Microsoft Windows platform. The freely available Microsoft .NET source code of EwE, however, provides a range of possibilities to use the model in different ways, to customize and extend the model, and to execute the model on different operating systems. We provide an overview of the EwE source code, its philosophy, and its technical capabilities, targeted to model builders and advanced users of the EwE software. We showcase novel scientific applications of the EwE model that have been facilitated because of the modular approach of the system. We also present three additional versions of EwE that have been written in different computer languages for dedicated purposes. Lastly, we provide an entry point for users for obtaining and using the source code for custom purposes.},

keywords = {Ecopath with Ecosim, ecosystem, fisheries, Food web model, model interoperability, Open source software},

pubstate = {published},

tppubtype = {article}

}

@article{christensen_representing_2014b,

title = {Representing Variable Habitat Quality in a Spatial Food Web Model},

author = {V. Christensen and M. Coll and J. Steenbeek and J. Buszowski and D. Chagaris and C. J. Walters},

url = {http://link.springer.com/article/10.1007/s10021-014-9803-3},

doi = {10.1007/s10021-014-9803-3},

issn = {1432-9840, 1435-0629},

year  = {2014},

date = {2014-08-01},

urldate = {2014-08-01},

journal = {Ecosystems},

volume = {17},

number = {8},

pages = {1397--1412},

note = {00000},

keywords = {Ecology, Ecopath, Ecospace, Environmental Management, Food web model, foraging capacity model, Geoecology/Natural Processes, habitat modeling, Hydrology/Water Resources, Plant Sciences, sampling, simulation model, species distribution model, Zoology},

pubstate = {published},

tppubtype = {article}

}

@article{christensenRepresentingVariableHabitat2014,

title = {Representing Variable Habitat Quality in a Spatial Food Web Model},

author = {Villy Christensen and Marta Coll and Jeroen Steenbeek and Joe Buszowski and Dave Chagaris and Carl J. Walters},

doi = {10.1007/s10021-014-9803-3},

issn = {1432-9840, 1435-0629},

year  = {2014},

date = {2014-08-01},

urldate = {2014-09-19},

journal = {Ecosystems},

pages = {1\textendash16},

abstract = {Why are marine species where they are? The scientific community is faced with an urgent need to understand aquatic ecosystem dynamics in the context of global change. This requires development of scientific tools with the capability to predict how biodiversity, natural resources, and ecosystem services will change in response to stressors such as climate change and further expansion of fishing. Species distribution models and ecosystem models are two methodologies that are being developed to further this understanding. To date, these methodologies offer limited capabilities to work jointly to produce integrated assessments that take both food web dynamics and spatial-temporal environmental variability into account. We here present a new habitat capacity model as an implementation of the spatial-temporal model Ecospace of the Ecopath with Ecosim approach. The new model offers the ability to drive foraging capacity of species from the cumulative impacts of multiple physical, oceanographic, and environmental factors such as depth, bottom type, temperature, salinity, oxygen concentrations, and so on. We use a simulation modeling procedure to evaluate sampling characteristics of the new habitat capacity model. This development bridges the gap between envelope environmental models and classic ecosystem food web models, progressing toward the ability to predict changes in marine ecosystems under scenarios of global change and explicitly taking food web direct and indirect interactions into account.},

keywords = {Ecology, Ecopath, Ecospace, Environmental Management, Food web model, foraging capacity model, Geoecology/Natural Processes, habitat modeling, Hydrology/Water Resources, Plant Sciences, sampling, simulation model, species distribution model, Zoology},

pubstate = {published},

tppubtype = {article}

}