diff --git a/joss.05731/10.21105.joss.05731.crossref.xml b/joss.05731/10.21105.joss.05731.crossref.xml new file mode 100644 index 0000000000..fe5f1e31c4 --- /dev/null +++ b/joss.05731/10.21105.joss.05731.crossref.xml @@ -0,0 +1,193 @@ + + + + 20240324T144123-b4731482c6f5a51b5e3870b4115466ab1265dcaa + 20240324144123 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 03 + 2024 + + + 9 + + 95 + + + + Viable North Sea (ViNoS): A NetLogo Agent-based Model +of German Small-scale Fisheries + + + + Carsten + Lemmen + https://orcid.org/0000-0003-3483-6036 + + + Sascha + Hokamp + https://orcid.org/0000-0002-2192-4013 + + + Serra + Örey + https://orcid.org/0000-0003-3483-6036 + + + Jürgen + Scheffran + https://orcid.org/0000-0002-7171-3062 + + + + 03 + 24 + 2024 + + + 5731 + + + 10.21105/joss.05731 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.7928199 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/5731 + + + + 10.21105/joss.05731 + https://joss.theoj.org/papers/10.21105/joss.05731 + + + https://joss.theoj.org/papers/10.21105/joss.05731.pdf + + + + + + Agent-based modeling of environmental conflict +and cooperation + BenDor + 10.1201/9781351106252 + 2019 + BenDor, T. K., & Scheffran, J. +(2019). Agent-based modeling of environmental conflict and cooperation +(1st ed.). CRC Press. +https://doi.org/10.1201/9781351106252 + + + The ODD protocol for describing agent-based +and other simulation models: A second update to improve clarity, +replication, and structural realism + Grimm + Journal of Artifical Societies and Social +Simulation + 2 + 23 + 10.18564/jasss.4259 + 2020 + Grimm, V., Railsback, S. F., +Vincenot, C. E., Berger, U., Gallagher, C., Deangelis, D. L., Edmonds, +B., Ge, J., Giske, J., Groeneveld, J., Johnston, A. S. A., Milles, A., +Nabe-Nielsen, J., Polhill, J. G., Radchuk, V., Rohwäder, M. S., +Stillman, R. A., Thiele, J. C., & Ayllón, D. (2020). The ODD +protocol for describing agent-based and other simulation models: A +second update to improve clarity, replication, and structural realism. +Journal of Artifical Societies and Social Simulation, 23(2). +https://doi.org/10.18564/jasss.4259 + + + NetLogo + Wilensky + 1999 + Wilensky, U. (1999). NetLogo. Center +for Connected Learning; Computer-Based Modeling, Northwestern +University. http://ccl.northwestern.edu/netlogo/ + + + REUSE software + 2023 + REUSE software. (2023). Free Software +Foundation Europe e.V. https://reuse.software + + + NetLogo how to add a legend? + arn + 2018 + arn, Sandoval, J., & Luke C. +(2018). NetLogo how to add a legend? Stackoverflow. +https://stackoverflow.com/questions/51328633/netlogo-how-to-add-a-legend + + + Behavioural diversity in fishing—towards a +next generation of fishery models + Wijermans + Fish and Fisheries + 5 + 21 + 10.1111/faf.12466 + 2020 + Wijermans, N., Boonstra, W. J., +Orach, K., Hentati-Sundberg, J., & Schlüter, M. (2020). Behavioural +diversity in fishing—towards a next generation of fishery models. Fish +and Fisheries, 21(5), 872–890. +https://doi.org/10.1111/faf.12466 + + + Modelling complex human systems: A fisheries +example + Allen + European Journal of Operational +Research + 2 + 30 + 10.1016/0377-2217(87)90092-0 + 0377-2217 + 1987 + Allen, P. M., & McGlade, J. M. +(1987). Modelling complex human systems: A fisheries example. European +Journal of Operational Research, 30(2), 147–167. +https://doi.org/10.1016/0377-2217(87)90092-0 + + + + + + diff --git a/joss.05731/10.21105.joss.05731.jats b/joss.05731/10.21105.joss.05731.jats new file mode 100644 index 0000000000..e118e1d9d8 --- /dev/null +++ b/joss.05731/10.21105.joss.05731.jats @@ -0,0 +1,416 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +5731 +10.21105/joss.05731 + +Viable North Sea (ViNoS): A NetLogo Agent-based Model of +German Small-scale Fisheries + + + +https://orcid.org/0000-0003-3483-6036 + +Lemmen +Carsten + + +* + + +https://orcid.org/0000-0002-2192-4013 + +Hokamp +Sascha + + + + +https://orcid.org/0000-0003-3483-6036 + +Örey +Serra + + + + +https://orcid.org/0000-0002-7171-3062 + +Scheffran +Jürgen + + + + + +Helmholtz-Zentrum Hereon, Institute of Coastal Systems - +Modeling and Analysis, Germany, carsten.lemmen@hereon.de + + + + +Universität Hamburg, Centre for Earth System Research and +Sustainability (CEN), Germany + + + + +Hochschule Bremerhaven, Research Cluster Life Sciences, +Bremerhaven, Germany + + + + +* E-mail: + + +7 +3 +2024 + +9 +95 +5731 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +NetLogo +Agent-based Model +ABM +North Sea +Fisheries +MuSSeL project +VIABLE +Plaice +Sole +Shrimp + + + + + + Summary +

Viable North Sea (ViNoS) is an Agent-based Model (ABM) of the + German Small-scale Fisheries. As a Social-Ecological Systems model it + focusses on the adaptive behaviour of fishers facing regulatory, + economic, and resource changes. Small-scale fisheries are an important + part both of the cultural perception of the German North Sea coast and + of its fishing industry. These fisheries are typically family-run + operations that use smaller boats and bottom trawling gear to catch a + variety of demersal species, foremost plaice, sole, and brown + shrimp.

+

Fishers in the North Sea face area competition with other uses of + the sea—long practiced ones like shipping, gas exploration and sand + extraction, and currently increasing ones like marine protection and + offshore wind farming: German authorities released a maritime spatial + plan implementing (1) the need for 30% of protection areas demanded by + the United Nations High Seas Treaty and (2) aiming at up to 70 GW of + domestic offshore wind power generation by 2045; the European Union is + aiming to reduce fisheries in all Marine Protected Areas. Fisheries in + the North Sea also have to adjust to the northward migration of their + established resources following the climate heating of the water. And + they have to re-evaluate their economic balance by figuring in the + foreseeable rise in oil price and the need for re-investing into their + aged fleet.

+ + + Statement of need +

Socio-economic fishery models are among the earliest application of + coupled human and natural systems modeling + (Allen + & McGlade, 1987). They have often concentrated on Maximum + Sustainable Yield, and have been neglecting adaptive behaviour and + diversity of fishers + (Wijermans + et al., 2020). The description of the patial, temporal and + structural adaptations of a fishery fleet is the purpose of the ViNoS + ABM. It is intended to be used for scenario development for future + sustainable fisheries. The ABM describes foremost

+ + +

where to fish and how far to go out to sea,

+ + +

how often to go out,

+ + +

what gear to use and what species to target.

+ + +

Its scope is the German North Sea small-scale fisheries. These + encompass some 300 vessels based and landing in German ports along the + North Sea coast and fishing in the German Bight, including but not + restricted to Germany’s exclusive economic zone. The target species + described by the model are currently limited to the commercially most + important ones in this sector: plaice, sole and brown shrimp; the + model is extensible to further target species like Norwegian lobster, + whiting, or sprat.

+

The intended audience of the ABM are marine researchers, educators + and government agencies concerned with spatial planning, environmental + status assessment, and climate change mitigation. The ABM can assist + in a stakeholder dialogue with tourism and fishers to contextualise + the complexity of the interactions between fisheries economics, + changing resources and regulatory restrictions.

+ + + Key features of the ABM +

As a NetLogo implementation, the model comprises a (frontend) user + Interface, its basic + Info documentation, and the (backend) + Code in a single integrated development + environment (IDE) provided by NetLogo + (Wilensky, + 1999, version 6 required), a Java-based portable ABM and system + dynamics simulation platform.

+

The backend (Code) features geospatial data + access and integration of multiple georeferenced and tabular data + sources, as well as integrating Web Mapping Services to describe the + grid-based environmental context. This environmental context is + dynamic in time, providing seasonal resource changes and dynamic area + closures.

+

Agents are boats, the gear they use, the strategies they employ, + and their prey. All agents are encapsulated in object-oriented design + as NetLogo breeds. The agents’ methods + implement the decision rules of agents and the resulting interactions + between them and with their gridded environment + (patches). Key interactions are the movement + rules of boats across the seascape, the harvesting of resources, and + the cost-benefit analysis of a catch. Adaptation occurs at the level + of changing priorities for fishing trips (i.e. gear selection and + target species, time and distance preferences) towards increasing + expected values of agents, according to the VIABLE model framework + (BenDor + & Scheffran, 2019).

+

The user Interface provides an interactive + environment, perusing all NetLogo’s graphical features. Informational + elements include a (georeferenced) map view, + and several histograms and temporal scatter panels. Interactive + elements include switches for toggling + information on and off, choosers to toggle + which information to show, buttons to control + the simulation and sliders to adjust boundary + conditions, such as the diesel price.

+ + + Notable programming and software development features +

This NetLogo model is a showcase of the integrated use of several + extensions to the base language, featuring, amongst other

+ + +

reading and writing of tabular data (csv + extension),

+ + +

import and export of Geographical Information System layers, + both ESRII raster .asc and vector + shapefiles .shp, both as local data and + interacting with Web Mapping Services and Web Feature Services, + from different projections and converted from other file formats + like NetCDF and geoTiff (using the gis + extension and python preprocessing),

+ + +

a real-time calendar using the time + extension and both tick-based (daily model timestep) as well as + discrete event scheduling for substepping.

+ + +

A notable programming feature is the integration of the legend with + the view, a feature that is lacking from the + default capabilities of NetLogo. There have been discussions on how to + implement a legend using the plot element and + using the bitmap extension + (arn + et al., 2018), but so far this is the only NetLogo model known + to the authors implementing a legend with the + view using NetLogo’s intrinsic + capabilities.

+

To date, most NetLogo models have not exploited continuous + integration (CI) and continuous deployment (CD). With our + implementation, we demonstrate how CI can be used for NetLogo by + making use of NetLogo’s BehaviorSpace tool that + runs a suite of unit tests. We also use + BehaviorSpace for the CD of generating the + resulting maps of fishing effort under different scenarios.

+ + + Model documentation and license +

The model is documented in short form in the NetLogo IDE’s + Info section. A full documentation follows the + Overview, Design concepts, and Details (ODD, + Grimm + et al., 2020) standard protocol for ABMs. This standard intends + to facilitate model replication and declares, amongst others, a + model’s purpose, entities, scales, processes and scheduling, and + initial and boundary data. The ViNoS ODD is available in the + repository as doc/odd/odd.md. Data from third + parties are licensed under a multitude of open source licenses. The + model, its results and own proprietary data are released under open + source licenses, mostly Apache 2.0 and CC-by-SA 4.0. A comprehensive + documentation of all licenses is provided via REUSE + Software + (2023).

+ + + Acknowledgements +

We acknowledge contributions from W. Nikolaus Probst, Marie Ryan, + Jieun Seo, Verena Mühlberger and Kai W. Wirtz for providing feedback, + data, fruitful discussions and for contributing to the ODD document. + We thank all members of the MuSSeL consortium making this software + relevant in a research context. The development of the model was made + possible by the grants 03F0862A, 03F0862C, 03F0862D, 03F0862E + “Multiple Stressors on North Sea Life” (MuSSeL) within the 3rd + Küstenforschung Nord-Ostsee (KüNO) call of the Forschung für + Nachhaltigkeit program of the Germany Bundesministerium für Bildung + und Forschung (BMBF). We are grateful for the open source community + that facilitated this research, amongst them the developers of and + contributors to NetLogo, Python, R, pandoc, and LaTeX.

+ + + + + + + + BenDorTodd K. + ScheffranJürgen + + Agent-based modeling of environmental conflict and cooperation + CRC Press + Boca Raton + 2019 + 1 + 10.1201/9781351106252 + + + + + + GrimmVolker + RailsbackSteven F. + VincenotChristian E. + BergerUta + GallagherCara + DeangelisDonald L. + EdmondsBruce + GeJiaqi + GiskeJarl + GroeneveldJürgen + JohnstonAlice S. A. + MillesAlexander + Nabe-NielsenJacob + PolhillJ. Gareth + RadchukViktoriia + RohwäderMarie Sophie + StillmanRichard A. + ThieleJan C. + AyllónDaniel + + The ODD protocol for describing agent-based and other simulation models: A second update to improve clarity, replication, and structural realism + Journal of Artifical Societies and Social Simulation + 2020 + 23 + 2 + 10.18564/jasss.4259 + + + + + + WilenskyUri + + NetLogo + Center for Connected Learning; Computer-Based Modeling, Northwestern University + Evanston, IL + 1999 + http://ccl.northwestern.edu/netlogo/ + + + + + REUSE software + Free Software Foundation Europe e.V. + 2023 + 20230402 + https://reuse.software + + + + + + arn + SandovalJavier + Luke C + + NetLogo how to add a legend? + Stackoverflow + 2018 + 20230403 + https://stackoverflow.com/questions/51328633/netlogo-how-to-add-a-legend + + + + + + WijermansNanda + BoonstraWiebren J. + OrachKirill + Hentati-SundbergJonas + SchlüterMaja + + Behavioural diversity in fishing—towards a next generation of fishery models + Fish and Fisheries + 2020 + 21 + 5 + https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12466 + 10.1111/faf.12466 + 872 + 890 + + + + + + AllenP. M. + McGladeJ. M. + + Modelling complex human systems: A fisheries example + European Journal of Operational Research + 1987 + 30 + 2 + 0377-2217 + https://www.sciencedirect.com/science/article/pii/0377221787900920 + 10.1016/0377-2217(87)90092-0 + 147 + 167 + + + + +
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