Developing multidisciplinary mechanistic models: challenges and approaches
Article Full Text (PDF)

Keywords

ecological modelling
mechanistic models
model complexity
model coupling
FAIR principles
research software

How to Cite

Vedder, D., Fischer, S. M., Wiegand, K., & Pe'er, G. (2024). Developing multidisciplinary mechanistic models: challenges and approaches. Socio-Environmental Systems Modelling, 6, 18701. https://doi.org/10.18174/sesmo.18701

Abstract

Current biodiversity models often struggle to represent the complexity of global crises, as the affected ecosystems are shaped by many different ecological, physical, and social processes. To understand these dynamics better, we will need to build larger and more complex ecological models, and couple ecological models to models produced by other disciplines, such as climate science, economics, or sociology. However, constructing such integrated models is a significant technical undertaking, which has received little attention by ecological modellers so far. We review literature from computer science and several other environmental modelling disciplines to identify common challenges and possible strategies when creating large integrated models. We show that there is a software-architectural trade-off between modularity and integration, where the former is required to keep the technical complexity of a model manageable, and the latter is desirable to represent the scientific complexity of a studied system. We then present and compare five different software engineering techniques for navigating this trade-off. Which technique is most suitable for a given model depends on the model’s aims and the available development resources. The larger a model becomes, the more important it is to use more advanced techniques, such as integrating models from different domains using a model coupling framework. Our review shows that ecological modellers can learn from other modelling disciplines, but also need to invest in increased software engineering expertise, if they want to build models that can represent the numerous processes affecting ecosystems and biodiversity loss.

Article Full Text (PDF)

References

Abelson, H., Sussman, G. J., & Sussman, J. (1996). Structure and interpretation of computer programs (2. ed). MIT Press.

Armstrong McKay, D. I., Staal, A., Abrams, J. F., Winkelmann, R., Sakschewski, B., Loriani, S., Fetzer, I., Cornell, S. E., Rockström, J., & Lenton, T. M. (2022). Exceeding 1.5°C global warming could trigger multiple climate tipping points. Science, 377(6611), eabn7950. https://doi.org/10.1126/science.abn7950

Balaban, G., Grytten, I., Rand, K. D., Scheffer, L., & Sandve, G. K. (2021). Ten simple rules for quick and dirty scientific programming. PLOS Computational Biology, 17(3), e1008549. https://doi.org/10.1371/journal.pcbi.1008549

Barton, C. M., Lee, A., Janssen, M. A., Porter, C., Greenberg, J., Swantek, L., Frank, K., Chen, M., & Jagers, H. R. A. (2022). How to make models more useful. Proceedings of the National Academy of Sciences, 119(35), 4.

Beck, F., & Diehl, S. (2011). On the congruence of modularity and code coupling. Proceedings of the 19th ACM SIGSOFT Symposium and the 13th European Conference on Foundations of Software Engineering, 354–364. https://doi.org/10.1145/2025113.2025162

Belete, G. F., Voinov, A., & Laniak, G. F. (2017). An overview of the model integration process: From pre-integration assessment to testing. Environmental Modelling & Software, 87, 49–63. https://doi.org/10.1016/j.envsoft.2016.10.013

Bell, A. R., Robinson, D. T., Malik, A., & Dewal, S. (2015). Modular ABM development for improved dissemination and training. Environmental Modelling & Software, 73, 189–200. https://doi.org/10.1016/j.envsoft.2015.07.016

Berger, U., Bell, A., Barton, C. M., Chappin, E., Dreßler, G., Filatova, T., Fronville, T., Lee, A., van Loon, E., Lorscheid, I., Meyer, M., Müller, B., Piou, C., Radchuk, V., Roxburgh, N., Schüler, L., Troost, C., Wijermans, N., Williams, T. G., … Grimm, V. (2024). Towards reusable building blocks for agent-based modelling and theory development. Environmental Modelling & Software, 175, 106003. https://doi.org/10.1016/j.envsoft.2024.106003

Bocedi, G., Palmer, S. C. F., Malchow, A.-K., Zurell, D., Watts, K., & Travis, J. M. J. (2021). RangeShifter 2.0: An extended and enhanced platform for modelling spatial eco-evolutionary dynamics and species’ responses to environmental changes. Ecography, 44(10), 1453–1462. https://doi.org/10.1111/ecog.05687

Bohn, F. J., Frank, K., & Huth, A. (2014). Of climate and its resulting tree growth: Simulating the productivity of temperate forests. Ecological Modelling, 278, 9–17. https://doi.org/10.1016/j.ecolmodel.2014.01.021

Brandmeyer, J. E., & Karimi, H. A. (2000). Coupling methodologies for environmental models. Environmental Modelling & Software, 15(5), 479–488. https://doi.org/10.1016/S1364-8152(00)00027-X

Brooks, F. (1986). No Silver Bullet – Essence and Accident in Software Engineering. In H.-J. Kugler (Ed.), Proceedings of the IFIP Tenth World Computing Conference (pp. 1069–1076). Elsevier Science B.V.

Brown, A., & Wilson, G. (Eds.). (2011). The Architecture of Open Source Applications. Creative Commons.

Bulatewicz, T., Yang, X., Peterson, J. M., Staggenborg, S., Welch, S. M., & Steward, D. R. (2010). Accessible integration of agriculture, groundwater, and economic models using the Open Modeling Interface (OpenMI): Methodology and initial results. Hydrol. Earth Syst. Sci., 14.

Cabral, J. S., Mendoza-Ponce, A., da Silva, A. P., Oberpriller, J., Mimet, A., Kieslinger, J., Berger, T., Blechschmidt, J., Brönner, M., Classen, A., Fallert, S., Hartig, F., Hof, C., Hoffmann, M., Knoke, T., Krause, A., Lewerentz, A., Pohle, P., Raeder, U., … Zurell, D. (2023). The road to integrate climate change projections with regional land-use–biodiversity models. People and Nature, n/a(n/a). https://doi.org/10.1002/pan3.10472

Cabral, J. S., Valente, L., & Hartig, F. (2017). Mechanistic simulation models in macroecology and biogeography: State-of-art and prospects. Ecography, 40(2), 267–280. https://doi.org/10.1111/ecog.02480

Churavy, V., Godoy, W. F., Bauer, C., Ranocha, H., Schlottke-Lakemper, M., Räss, L., Blaschke, J., Giordano, M., Schnetter, E., Omlin, S., Vetter, J. S., & Edelman, A. (2022, November 10). Bridging HPC Communities through the Julia Programming Language. https://doi.org/10.48550/arXiv.2211.02740

Cohen, J., Katz, D. S., Barker, M., Hong, N. C., Haines, R., & Jay, C. (2021). The Four Pillars of Research Software Engineering. IEEE Software, 38(1), 97–105. IEEE Software. https://doi.org/10.1109/MS.2020.2973362

David, O., Ascough, J. C., Lloyd, W., Green, T. R., Rojas, K. W., Leavesley, G. H., & Ahuja, L. R. (2013). A software engineering perspective on environmental modeling framework design: The Object Modeling System. Environmental Modelling & Software, 39, 201–213. https://doi.org/10.1016/j.envsoft.2012.03.006

DeAngelis, D. L., & Grimm, V. (2014). Individual-based models in ecology after four decades. F1000prime Reports, 6, 39. https://doi.org/10.12703/P6-39

Dijkstra, E. W. (1972). The humble programmer. Communications of the ACM, 15(10), 859–866. https://doi.org/10.1145/355604.361591

Dislich, C., & Huth, A. (2012). Modelling the impact of shallow landslides on forest structure in tropical montane forests. Ecological Modelling, 239, 40–53. https://doi.org/10.1016/j.ecolmodel.2012.04.016

Edwards, P. N. (2011). History of climate modeling. WIREs Climate Change, 2(1), 128–139. https://doi.org/10.1002/wcc.95

Enders, A., Martre, P., Raynal, H., Athanasiadis, I., Donatelli, M., Fumagalli, D., Holzworth, D., Stöckle, C., & Hoogenboom, G. (2018). Agricultural Model Exchange Initiative (AMEI). 61. https://scholarsarchive.byu.edu/iemssconference/2018/Stream-A/61

Evans, L. C., Sibly, R. M., Thorbek, P., Sims, I., Oliver, T. H., & Walters, R. J. (2019). Quantifying the effectiveness of agri-environment schemes for a grassland butterfly using individual-based models. Ecological Modelling, 411, 108798. https://doi.org/10.1016/j.ecolmodel.2019.108798

Eyring, V., Bony, S., Meehl, G. A., Senior, C. A., Stevens, B., Stouffer, R. J., & Taylor, K. E. (2016). Overview of the Coupled Model Intercomparison Project Phase 6 (CMIP6) experimental design and organization. Geoscientific Model Development, 9(5), 1937–1958. https://doi.org/10.5194/gmd-9-1937-2016

Farahbakhsh, I., Bauch, C. T., & Anand, M. (2022). Modelling coupled human–environment complexity for the future of the biosphere: Strengths, gaps and promising directions. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1857), 20210382. https://doi.org/10.1098/rstb.2021.0382

Farrell, K. J., & Carey, C. C. (2018). Power, pitfalls, and potential for integrating computational literacy into undergraduate ecology courses. Ecology and Evolution, 8(16), 7744–7751. https://doi.org/10.1002/ece3.4363

Fer, I., Gardella, A. K., Shiklomanov, A. N., Campbell, E. E., Cowdery, E. M., De Kauwe, M. G., Desai, A., Duveneck, M. J., Fisher, J. B., Haynes, K. D., Hoffman, F. M., Johnston, M. R., Kooper, R., LeBauer, D. S., Mantooth, J., Parton, W. J., Poulter, B., Quaife, T., Raiho, A., … Dietze, M. C. (2021). Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data-model integration. Global Change Biology, 27(1), 13–26. https://doi.org/10.1111/gcb.15409

Filazzola, A., & Lortie, C. (2022). A call for clean code to effectively communicate science. Methods in Ecology and Evolution, n/a(n/a). https://doi.org/10.1111/2041-210X.13961

Fischer, R. (2021). The Long-Term Consequences of Forest Fires on the Carbon Fluxes of a Tropical Forest in Africa. Applied Sciences, 11(10), 4696. https://doi.org/10.3390/app11104696

Fischer, R., Bohn, F., Dantas De Paula, M., Dislich, C., Groeneveld, J., Gutiérrez, A. G., Kazmierczak, M., Knapp, N., Lehmann, S., Paulick, S., Pütz, S., Rödig, E., Taubert, F., Köhler, P., & Huth, A. (2016). Lessons learned from applying a forest gap model to understand ecosystem and carbon dynamics of complex tropical forests. Ecological Modelling, 326, 124–133. https://doi.org/10.1016/j.ecolmodel.2015.11.018

Fust, P., & Schlecht, E. (2018). Integrating spatio-temporal variation in resource availability and herbivore movements into rangeland management: RaMDry—An agent-based model on livestock feeding ecology in a dynamic, heterogeneous, semi-arid environment. Ecological Modelling, 369, 13–41. https://doi.org/10.1016/j.ecolmodel.2017.10.017

Gregersen, J. B., Gijsbers, P. J. A., & Westen, S. J. P. (2007). OpenMI: Open modelling interface. Journal of Hydroinformatics, 9(3), 175–191. https://doi.org/10.2166/hydro.2007.023

Grimm, V., Ayllón, D., & Railsback, S. F. (2017). Next-Generation Individual-Based Models Integrate Biodiversity and Ecosystems: Yes We Can, and Yes We Must. Ecosystems, 20(2), 229–236. https://doi.org/10.1007/s10021-016-0071-2

Grimm, V., Johnston, A. S. A., Thulke, H.-H., Forbes, V. E., & Thorbek, P. (2020). Three questions to ask before using model outputs for decision support. Nature Communications, 11(1, 1), 4959. https://doi.org/10.1038/s41467-020-17785-2

Grimm, V., & Railsback, S. F. (2005). Individual-based Modeling and Ecology. Princeton University Press.

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 Artificial Societies and Social Simulation, 23(2), 7. https://doi.org/10.18564/jasss.4259

Guillem, E. E., Murray-Rust, D., Robinson, D. T., Barnes, A., & Rounsevell, M. D. A. (2015). Modelling farmer decision-making to anticipate tradeoffs between provisioning ecosystem services and biodiversity. Agricultural Systems, 137, 12–23. https://doi.org/10.1016/j.agsy.2015.03.006

Gutiérrez, A. G., Armesto, J. J., Díaz, M. F., & Huth, A. (2014). Increased Drought Impacts on Temperate Rainforests from Southern South America: Results of a Process-Based, Dynamic Forest Model. PLoS ONE, 9(7), e103226. https://doi.org/10.1371/journal.pone.0103226

Hagen, O., Flück, B., Fopp, F., Cabral, J. S., Hartig, F., Pontarp, M., Rangel, T. F., & Pellissier, L. (2021). Gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity. PLOS Biology, 19(7), e3001340. https://doi.org/10.1371/journal.pbio.3001340

Harfoot, M. B. J., Newbold, T., Tittensor, D. P., Emmott, S., Hutton, J., Lyutsarev, V., Smith, M. J., Scharlemann, J. P. W., & Purves, D. W. (2014). Emergent Global Patterns of Ecosystem Structure and Function from a Mechanistic General Ecosystem Model. PLOS Biology, 12(4), e1001841. https://doi.org/10.1371/journal.pbio.1001841

Harfoot, M. B. J., Tittensor, D. P., Newbold, T., McInerny, G., Smith, M. J., & Scharlemann, J. P. W. (2014). Integrated assessment models for ecologists: The present and the future. Global Ecology and Biogeography, 23(2), 124–143. https://doi.org/10.1111/geb.12100

Harpham, Q. K., Hughes, A., & Moore, R. V. (2019). Introductory overview: The OpenMI 2.0 standard for integrating numerical models. Environmental Modelling & Software, 122, 104549. https://doi.org/10.1016/j.envsoft.2019.104549

Hasselbring, W., Carr, L., Hettrick, S., Packer, H., & Tiropanis, T. (2020). From FAIR research data toward FAIR and open research software. It - Information Technology, 62(1), 39–47. https://doi.org/10.1515/itit-2019-0040

Hill, C., DeLuca, C., Balaji, Suarez, M., & Da Silva, A. (2004). The architecture of the earth system modeling framework. Computing in Science & Engineering, 6(1), 18–28. https://doi.org/10.1109/MCISE.2004.1255817

Hoeks, S., Tucker, M. A., Huijbregts, M. A. J., Harfoot, M. B. J., Bithell, M., & Santini, L. (2021). MadingleyR: An R package for mechanistic ecosystem modelling. Global Ecology and Biogeography, 30(9), 1922–1933. https://doi.org/10.1111/geb.13354

Holzworth, D. P., Huth, N. I., & deVoil, P. G. (2011). Simple software processes and tests improve the reliability and usefulness of a model. Environmental Modelling & Software, 26(4), 510–516. https://doi.org/10.1016/j.envsoft.2010.10.014

IPBES. (2016). The Methodological Assessment Report on Scenarios and Models of Biodiversity and Ecosystem Services (p. 348). ecretariat of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. https://ipbes.net/sites/default/files/downloads/pdf/2016.methodological_assessment_report_scenarios_models.pdf

Janssen, M. A., Alessa, L. N., Barton, M., Bergin, S., & Lee, A. (2008). Towards a Community Framework for Agent-Based Modelling. Journal of Artificial Societies and Social Simulation, 11(26), 1–13. https://www.jasss.org/11/2/6/6.pdf

Janssen, M. A., Pritchard, C., & Lee, A. (2020). On code sharing and model documentation of published individual and agent-based models. Environmental Modelling & Software, 134, 104873. https://doi.org/10.1016/j.envsoft.2020.104873

Janssen, S., Athanasiadis, I. N., Bezlepkina, I., Knapen, R., Li, H., Domínguez, I. P., Rizzoli, A. E., & van Ittersum, M. K. (2011). Linking models for assessing agricultural land use change. Computers and Electronics in Agriculture, 76(2), 148–160. https://doi.org/10.1016/j.compag.2010.10.011

Jetz, W., McGeoch, M. A., Guralnick, R., Ferrier, S., Beck, J., Costello, M. J., Fernandez, M., Geller, G. N., Keil, P., Merow, C., Meyer, C., Muller-Karger, F. E., Pereira, H. M., Regan, E. C., Schmeller, D. S., & Turak, E. (2019). Essential biodiversity variables for mapping and monitoring species populations. Nature Ecology & Evolution, 3(4, 4), 539–551. https://doi.org/10.1038/s41559-019-0826-1

Johanson, A., & Hasselbring, W. (2018). Software Engineering for Computational Science: Past, Present, Future. Computing in Science & Engineering, 20(2), 90–109. Computing in Science & Engineering. https://doi.org/10.1109/MCSE.2018.021651343

Kim, H., Rosa, I. M. D., Alkemade, R., Leadley, P., Hurtt, G., Popp, A., van Vuuren, D. P., Anthoni, P., Arneth, A., Baisero, D., Caton, E., Chaplin-Kramer, R., Chini, L., De Palma, A., Di Fulvio, F., Di Marco, M., Espinoza, F., Ferrier, S., Fujimori, S., … Pereira, H. M. (2018). A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios. Geoscientific Model Development. https://doi.org/10.5194/gmd-2018-115

Knapen, R., Janssen, S., Roosenschoon, O., Verweij, P., de Winter, W., Uiterwijk, M., & Wien, J.-E. (2013). Evaluating OpenMI as a model integration platform across disciplines. Environmental Modelling & Software, 39, 274–282. https://doi.org/10.1016/j.envsoft.2012.06.011

Köhler, P., & Huth, A. (1998). The effects of tree species grouping in tropical rainforest modelling: Simulations with the individual-based model Formind. Ecological Modelling, 109(3), 301–321. https://doi.org/10.1016/S0304-3800(98)00066-0

Lange, M., Müller, S., Fischer, T., König, S., Rojas, J. J. L., Kelbling, M., Thober, S., & Attinger, S. (2023). FINAM (Version 0.4) [Computer software]. Helmholtz Center for Environmental Research - UFZ. https://finam.pages.ufz.de/

Le, Q. B., Park, S. J., Vlek, P. L. G., & Cremers, A. B. (2008). Land-Use Dynamic Simulator (LUDAS): A multi-agent system model for simulating spatio-temporal dynamics of coupled human–landscape system. I. Structure and theoretical specification. Ecological Informatics, 3(2), 135–153. https://doi.org/10.1016/j.ecoinf.2008.04.003

Lee, B. D. (2018). Ten simple rules for documenting scientific software. PLOS Computational Biology, 14(12), e1006561. https://doi.org/10.1371/journal.pcbi.1006561

Lee, J.-Y., Marotzke, J., Bala, G., Cao, L., Corti, S., Dunne, J. P., Engelbrecht, F., Fischer, E., Fyfe, J. C., Jones, C., Maycock, A., Mutemi, J., Ndiaye, O., Panickal, S., & Zhou, T. (2021). Future Global Climate: Scenario-based Projections and Near-term Information. In V. Masson-Delmotte, P. Zhai, A. Pirani, S. L. Connors, C. Péan, S. Berger, N. Caud, Y. Chen, L. Goldfarb, M. I. Gomis, M. Huang, K. Leitzell, E. Lonnoy, J. B. R. Matthews, T. K. Maycock, T. Waterfield, O. Yelekci, R. Yu, & B. Zhou (Eds.), Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (pp. 553–672). Cambridge University Press.

Lehmann, S., & Huth, A. (2015). Fast calibration of a dynamic vegetation model with minimum observation data. Ecological Modelling, 301, 98–105. https://doi.org/10.1016/j.ecolmodel.2015.01.013

Leidinger, L., Vedder, D., & Cabral, J. S. (2021). Temporal environmental variation may impose differential selection on both genomic and ecological traits. Oikos, 130(7), 1100–1115. https://doi.org/10.1111/oik.08172

Lippe, M., Bithell, M., Gotts, N., Natalini, D., Barbrook-Johnson, P., Giupponi, C., Hallier, M., Hofstede, G. J., Le Page, C., Matthews, R. B., Schlüter, M., Smith, P., Teglio, A., & Thellmann, K. (2019). Using agent-based modelling to simulate social-ecological systems across scales. GeoInformatica, 23(2), 269–298. https://doi.org/10.1007/s10707-018-00337-8

Lorscheid, I., & Meyer, M. (2016). Divide and conquer: Configuring submodels for valid and efficient analyses of complex simulation models. Ecological Modelling, 326, 152–161. https://doi.org/10.1016/j.ecolmodel.2015.11.013

Maji, A. K., Gorenstein, L., & Lentner, G. (2020). Demystifying Python Package Installation with conda-env-mod. 2020 IEEE/ACM International Workshop on HPC User Support Tools (HUST) and Workshop on Programming and Performance Visualization Tools (ProTools), 27–37. https://doi.org/10.1109/HUSTProtools51951.2020.00011

Malawska, A., & Topping, C. J. (2018). Applying a biocomplexity approach to modelling farmer decision-making and land use impacts on wildlife. Journal of Applied Ecology, 55(3), 1445–1455. https://doi.org/10.1111/1365-2664.13024

Malawska, A., Topping, C. J., & Nielsen, H. Ø. (2014). Why do we need to integrate farmer decision making and wildlife models for policy evaluation? Land Use Policy, 38, 732–740. https://doi.org/10.1016/j.landusepol.2013.10.025

Malchow, A., Bocedi, G., Palmer, S. C. F., Travis, J. M. J., & Zurell, D. (2021). RangeShiftR: An R package for individual‐based simulation of spatial eco‐evolutionary dynamics and species’ responses to environmental changes. Ecography, 44(10), 1443–1452. https://doi.org/10.1111/ecog.05689

Manabe, S. (2019). Role of greenhouse gas in climate change. Tellus A: Dynamic Meteorology and Oceanography, 71(1), 1620078. https://doi.org/10.1080/16000870.2019.1620078

Martin, R. C. (Ed.). (2009). Clean code: A handbook of agile software craftsmanship. Prentice Hall.

Marwick, B., Boettiger, C., & Mullen, L. (2018). Packaging Data Analytical Work Reproducibly Using R (and Friends). The American Statistician, 72(1), 80–88. https://doi.org/10.1080/00031305.2017.1375986

McConnell, S. (2004). Code Complete (2nd ed). Microsoft Press.

McIntire, E. J. B., Chubaty, A. M., Cumming, S. G., Andison, D., Barros, C., Boisvenue, C., Haché, S., Luo, Y., Micheletti, T., & Stewart, F. E. C. (2022). PERFICT: A Re-imagined foundation for predictive ecology. Ecology Letters, 25(6), 1345–1351. https://doi.org/10.1111/ele.13994

Mislan, K. A. S., Heer, J. M., & White, E. P. (2016). Elevating The Status of Code in Ecology. Trends in Ecology & Evolution, 31(1), 4–7. https://doi.org/10.1016/j.tree.2015.11.006

Nowogrodzki, A. (2019). Tips for Open-Source Software Support. Nature, 571(7763, 7763), 133–134. https://doi.org/10.1038/d41586-019-02046-0

O’Sullivan, D., Evans, T., Manson, S., Metcalf, S., Ligmann-Zielinska, A., & Bone, C. (2016). Strategic directions for agent-based modeling: Avoiding the YAAWN syndrome. Journal of Land Use Science, 11(2), 177–187. https://doi.org/10.1080/1747423X.2015.1030463

Pan, H., & Chen, Z. (2021). Crop Growth Modeling and Yield Forecasting. In L. Di & B. Üstündağ (Eds.), Agro-geoinformatics: Theory and Practice (pp. 205–220). Springer International Publishing. https://doi.org/10.1007/978-3-030-66387-2_11

Perez-Riverol, Y., Gatto, L., Wang, R., Sachsenberg, T., Uszkoreit, J., Leprevost, F. da V., Fufezan, C., Ternent, T., Eglen, S. J., Katz, D. S., Pollard, T. J., Konovalov, A., Flight, R. M., Blin, K., & Vizcaíno, J. A. (2016). Ten Simple Rules for Taking Advantage of Git and GitHub. PLOS Computational Biology, 12(7), e1004947. https://doi.org/10.1371/journal.pcbi.1004947

Pilowsky, J. A., Colwell, R. K., Rahbek, C., & Fordham, D. A. (2022). Process-explicit models reveal the structure and dynamics of biodiversity patterns. Science Advances, 8(31), eabj2271. https://doi.org/10.1126/sciadv.abj2271

Piorr, A., Ungaro, F., Ciancaglini, A., Happe, K., Sahrbacher, A., Sattler, C., Uthes, S., & Zander, P. (2009). Integrated assessment of future CAP policies: Land use changes, spatial patterns and targeting. Environmental Science & Policy, 12(8), 1122–1136. https://doi.org/10.1016/j.envsci.2009.01.001

Pörtner, H.-O., Scholes, R. J., Agard, J., Archer, E., Arneth, A., Bai, X., Barnes, D., Burrows, M., Chan, L., Cheung, W. L. (William)., Diamond, S., Donatti, C., Duarte, C., Eisenhauer, N., Foden, W., Gasalla, M. A., Handa, C., Hickler, T., Hoegh-Guldberg, O., … Ngo, H. (2021). Scientific outcome of the IPBES-IPCC co-sponsored workshop on biodiversity and climate change. IPBES secretariat. https://doi.org/10.5281/zenodo.5101125

Prabhu, P., Jablin, T. B., Raman, A., Zhang, Y., Huang, J., Kim, H., Johnson, N. P., Liu, F., Ghosh, S., Beard, S., Oh, T., Zoufaly, M., Walker, D., & August, D. I. (2011). A survey of the practice of computational science. State of the Practice Reports, 1–12. https://doi.org/10.1145/2063348.2063374

Pütz, S., Groeneveld, J., Alves, L. F., Metzger, J. P., & Huth, A. (2011). Fragmentation drives tropical forest fragments to early successional states: A modelling study for Brazilian Atlantic forests. Ecological Modelling, 222(12), 1986–1997. https://doi.org/10.1016/j.ecolmodel.2011.03.038

Ram, K., Boettiger, C., Chamberlain, S., Ross, N., Salmon, M., & Butland, S. (2019). A Community of Practice Around Peer Review for Long-Term Research Software Sustainability. Computing in Science Engineering, 21(2), 59–65. Computing in Science Engineering. https://doi.org/10.1109/MCSE.2018.2882753

Reidsma, P., Janssen, S., Jansen, J., & van Ittersum, M. K. (2018). On the development and use of farm models for policy impact assessment in the European Union – A review. Agricultural Systems, 159, 111–125. https://doi.org/10.1016/j.agsy.2017.10.012

Robinson, D. T., Di Vittorio, A., Alexander, P., Arneth, A., Barton, C. M., Brown, D. G., Kettner, A., Lemmen, C., O’Neill, B. C., Janssen, M., Pugh, T. A. M., Rabin, S. S., Rounsevell, M., Syvitski, J. P., Ullah, I., & Verburg, P. H. (2018). Modelling feedbacks between human and natural processes in the land system. Earth System Dynamics, 9(2), 895–914. https://doi.org/10.5194/esd-9-895-2018

Rollins, N. D., Barton, C. M., Bergin, S., Janssen, M. A., & Lee, A. (2014). A Computational Model Library for publishing model documentation and code. Environmental Modelling & Software, 61, 59–64. https://doi.org/10.1016/j.envsoft.2014.06.022

Romero-Mujalli, D., Jeltsch, F., & Tiedemann, R. (2019). Individual-based modeling of eco-evolutionary dynamics: State of the art and future directions. Regional Environmental Change, 19(1), 1–12. https://doi.org/10.1007/s10113-018-1406-7

Ropella, G. E., Railsback, S. F., & Jackson, S. K. (2002). Software Engineering Considerations for Individual-Based Models. Natural Resource Modeling, 15(1), 5–22. https://doi.org/10.1111/j.1939-7445.2002.tb00077.x

Rosenzweig, C., Arnell, N. W., Ebi, K. L., Lotze-Campen, H., Raes, F., Rapley, C., Smith, M. S., Cramer, W., Frieler, K., Reyer, C. P. O., Schewe, J., Vuuren, D. van, & Warszawski, L. (2017). Assessing inter-sectoral climate change risks: The role of ISIMIP. Environmental Research Letters, 12(1), 010301. https://doi.org/10.1088/1748-9326/12/1/010301

Rosenzweig, C., Jones, J. W., Hatfield, J. L., Ruane, A. C., Boote, K. J., Thorburn, P., Antle, J. M., Nelson, G. C., Porter, C., Janssen, S., Asseng, S., Basso, B., Ewert, F., Wallach, D., Baigorria, G., & Winter, J. M. (2013). The Agricultural Model Intercomparison and Improvement Project (AgMIP): Protocols and pilot studies. Agricultural and Forest Meteorology, 170, 166–182. https://doi.org/10.1016/j.agrformet.2012.09.011

Samaniego, L., Kumar, R., & Attinger, S. (2010). Multiscale parameter regionalization of a grid-based hydrologic model at the mesoscale: MULTISCALE PARAMETER REGIONALIZATION. Water Resources Research, 46(5). https://doi.org/10.1029/2008WR007327

Sanders, R., & Kelly, D. (2008). Dealing with Risk in Scientific Software Development. IEEE Software, 25(4), 21–28. https://doi.org/10.1109/MS.2008.84

Scheller, R. M., Sturtevant, B. R., Gustafson, E. J., Ward, B. C., & Mladenoff, D. J. (2010). Increasing the reliability of ecological models using modern software engineering techniques. Frontiers in Ecology and the Environment, 8(5), 253–260. https://doi.org/10.1890/080141

Schmidt, A., Necpalova, M., Zimmermann, A., Mann, S., Six, J., & Mack, G. (2017). Direct and Indirect Economic Incentives to Mitigate Nitrogen Surpluses: A Sensitivity Analysis. Journal of Artificial Societies and Social Simulation, 20(4), 77. https://doi.org/10.18564/jasss.3477

Schouten, R., Vesk, P. A., & Kearney, M. R. (2020). Integrating dynamic plant growth models and microclimates for species distribution modelling. Ecological Modelling, 435, 109262. https://doi.org/10.1016/j.ecolmodel.2020.109262

Schreinemachers, P., & Berger, T. (2011). An agent-based simulation model of human–environment interactions in agricultural systems. Environmental Modelling & Software, 26(7), 845–859. https://doi.org/10.1016/j.envsoft.2011.02.004

Shrestha, N. K., Leta, O. T., De Fraine, B., Garcia-Armisen, T., Ouattara, N. K., Servais, P., van Griensven, A., & Bauwens, W. (2013). Modelling Escherichia coli dynamics in the river Zenne (Belgium) using an OpenMI based integrated model. Journal of Hydroinformatics, 16(2), 354–374. https://doi.org/10.2166/hydro.2013.171

Sibly, R. M., Grimm, V., Martin, B. T., Johnston, A. S. A., Kułakowska, K., Topping, C. J., Calow, P., Nabe-Nielsen, J., Thorbek, P., & DeAngelis, D. L. (2013). Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution, 4(2), 151–161. https://doi.org/10.1111/2041-210x.12002

Sieger, C. S., & Hovestadt, T. (2021). The effect of landscape structure on the evolution of two alternative dispersal strategies. Ecological Processes, 10(1), 73. https://doi.org/10.1186/s13717-021-00343-z

Simon, R. N., & Fortin, D. (2020). Crop raiders in an ecological trap: Optimal foraging individual-based modeling quantifies the effect of alternate crops. Ecological Applications, 30(5), e02111. https://doi.org/10.1002/eap.2111

Stillman, R. A., Wood, K. A., & Goss-Custard, J. D. (2016). Deriving simple predictions from complex models to support environmental decision-making. Ecological Modelling, 326, 134–141. https://doi.org/10.1016/j.ecolmodel.2015.04.014

Sun, Z., Lorscheid, I., Millington, J. D., Lauf, S., Magliocca, N. R., Groeneveld, J., Balbi, S., Nolzen, H., Müller, B., Schulze, J., & Buchmann, C. M. (2016). Simple or complicated agent-based models? A complicated issue. Environmental Modelling & Software, 86, 56–67. https://doi.org/10.1016/j.envsoft.2016.09.006

Synes, N. W., Brown, C., Palmer, S. C. F., Bocedi, G., Osborne, P. E., Watts, K., Franklin, J., & Travis, J. M. J. (2019). Coupled land use and ecological models reveal emergence and feedbacks in socio‐ecological systems. Ecography, 42(4), 814–825. https://doi.org/10.1111/ecog.04039

Theurich, G., DeLuca, C., Campbell, T., Liu, F., Saint, K., Vertenstein, M., Chen, J., Oehmke, R., Doyle, J., Whitcomb, T., Wallcraft, A., Iredell, M., Black, T., Silva, A. M. D., Clune, T., Ferraro, R., Li, P., Kelley, M., Aleinov, I., … Dunlap, R. (2016). The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability. Bulletin of the American Meteorological Society, 97(7), 1229–1247. https://doi.org/10.1175/BAMS-D-14-00164.1

Topping, C. J. (2011). Evaluation of wildlife management through organic farming. Ecological Engineering, 37(12), 2009–2017. https://doi.org/10.1016/j.ecoleng.2011.08.010

Topping, C. J. (2022). ALMaSS - the animal, landscape and man simulation system [Computer software]. Department of Wildlife Ecology & Biodiversity, Aarhus University. https://gitlab.com/ChrisTopping/ALMaSS_all

Topping, C. J., Alrøe, H. F., Farrell, K. N., & Grimm, V. (2015). Per Aspera ad Astra: Through Complex Population Modeling to Predictive Theory. The American Naturalist, 186(5), 669–674. https://doi.org/10.1086/683181

Topping, C. J., Hansen, T. S., Jensen, T. S., Jepsen, J. U., Nikolajsen, F., & Odderskær, P. (2003). ALMaSS, an agent-based model for animals in temperate European landscapes. Ecological Modelling, 167(1), 65–82. https://doi.org/10.1016/S0304-3800(03)00173-X

Urban, M. C., Bocedi, G., Hendry, A. P., Mihoub, J.-B., Pe’er, G., Singer, A., Bridle, J. R., Crozier, L. G., De Meester, L., Godsoe, W., Gonzalez, A., Hellmann, J. J., Holt, R. D., Huth, A., Johst, K., Krug, C. B., Leadley, P. W., Palmer, S. C. F., Pantel, J. H., … Travis, J. M. J. (2016). Improving the forecast for biodiversity under climate change. Science, 353(6304), aad8466. https://doi.org/10.1126/science.aad8466

Urban, M. C., Travis, J. M. J., Zurell, D., Thompson, P. L., Synes, N. W., Scarpa, A., Peres-Neto, P. R., Malchow, A.-K., James, P. M. A., Gravel, D., De Meester, L., Brown, C., Bocedi, G., Albert, C. H., Gonzalez, A., & Hendry, A. P. (2022). Coding for Life: Designing a Platform for Projecting and Protecting Global Biodiversity. BioScience, 72(1), 91–104. https://doi.org/10.1093/biosci/biab099

Vable, A. M., Diehl, S. F., & Glymour, M. M. (2021). Code Review as a Simple Trick to Enhance Reproducibility, Accelerate Learning, and Improve the Quality of Your Team’s Research. American Journal of Epidemiology, 190(10), 2172–2177. https://doi.org/10.1093/aje/kwab092

van Ittersum, M. K., Ewert, F., Heckelei, T., Wery, J., Alkan Olsson, J., Andersen, E., Bezlepkina, I., Brouwer, F., Donatelli, M., Flichman, G., Olsson, L., Rizzoli, A. E., van der Wal, T., Wien, J. E., & Wolf, J. (2008). Integrated assessment of agricultural systems – A component-based framework for the European Union (SEAMLESS). Agricultural Systems, 96(1-3), 150–165. https://doi.org/10.1016/j.agsy.2007.07.009

Vedder, D., Ankenbrand, M., & Cabral, J. S. (2021). Dealing with software complexity in individual-based models. Methods in Ecology and Evolution, 12(12), 2324–2333. https://doi.org/10.1111/2041-210X.13716

Vedder, D., Leidinger, L., & Sarmento Cabral, J. (2021). Propagule pressure and an invasion syndrome determine invasion success in a plant community model. Ecology and Evolution, 11(23), 17106–17116. https://doi.org/10.1002/ece3.8348

Vedder, D., Lens, L., Martin, C. A., Pellikka, P., Adhikari, H., Heiskanen, J., Engler, J. O., & Sarmento Cabral, J. (2022). Hybridization may aid evolutionary rescue of an endangered East African passerine. Evolutionary Applications, 15(7), 1177–1188. https://doi.org/10.1111/eva.13440

Vincenot, C. E. (2018). How new concepts become universal scientific approaches: Insights from citation network analysis of agent-based complex systems science. Proceedings of the Royal Society B: Biological Sciences, 285(1874), 20172360. https://doi.org/10.1098/rspb.2017.2360

Will, M., Dressler, G., Kreuer, D., Thulke, H.-H., Grêt‐Regamey, A., & Müller, B. (2021). How to make socio-environmental modelling more useful to support policy and management? People and Nature, 00, 1–13. https://doi.org/10.1002/pan3.10207

Wilson, G., Aruliah, D. A., Brown, C. T., Chue Hong, N. P., Davis, M., Guy, R. T., Haddock, S. H. D., Huff, K. D., Mitchell, I. M., Plumbley, M. D., Waugh, B., White, E. P., & Wilson, P. (2014). Best Practices for Scientific Computing. PLoS Biology, 12(1), 1–7. https://doi.org/10.1371/journal.pbio.1001745

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Copyright (c) 2024 Daniel Vedder, Samuel M. Fischer, Kerstin Wiegand, Guy Pe'er