journal article·2024-12-26Open access

Integrating Multi-Model Simulations to Address Partial Observability in Population Dynamics: A Python-Based Ecological Tool

Yide Yu, Huijie Li, Yue Liu, Yan Ma

Applied Sciences· Volume 15· Issue 1

Abstract

Species richness is a crucial factor in maintaining ecological balance and promoting ecosystem services. However, simulating population dynamics is a complex task that requires a comprehensive understanding of ecological systems. The current tools for wildlife research face three major challenges: insufficient multi-view assessment, a high learning curve, and a lack of seamless secondary development with Python. To address these issues, we developed a novel software tool named WAPET (Wildlife Analysis and Population Ecology Tool) (Python 3.10.12). WAPET integrates Monte Carlo simulation with ecological models, including Logistic Growth, Random Walk, and Cellular Automata, to provide a multi-perspective assessment of ecological systems. Our tool employs a fully parameterized input paradigm, allowing users without coding to easily explore simulations. Additionally, WAPET’s development is entirely Python-based, utilizing PySide6 and Mesa libraries and enabling seamless development in Python environments. Our contributions include the following: (I) integrating multiple ecological models for a comprehensive understanding of ecological processes, (II) developing a no-code mode of human–computer interaction for biodiversity stakeholders and researchers, and (III) implementing a Python-based framework for easy extension and customization. WAPET bridges the gap between comprehensive modeling capabilities and user-friendly interfaces, positioning itself as a versatile tool for both experienced researchers and non-computational stakeholders in biodiversity decision-making processes.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Species Distribution and Climate Change · Ecosystem dynamics and resilience · Evolution and Genetic Dynamics

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR 999078, China

BUPT Network Information Center, Beijing University of Posts and Telecommunications, Beijing 100876, China

References (41)

Show source-provided references
1. The demographic consequences of releasing a population of red deer from culling10.1890/03-0009 ↗
2. Biodiversity and ecosystem services: A multilayered relationship10.1016/j.tree.2011.08.006 ↗
3. Ecological forecasts: An emerging imperative10.1126/science.293.5530.657 ↗
4. Habitat loss, the dynamics of biodiversity, and a perspective on conservation10.1007/s13280-011-0147-3 ↗
5. Exploratory modeling for policy analysis10.1287/opre.41.3.435 ↗
6. Shamsaddini, S., Ahmadi Gohari, M., Kamyabi, H., Nasibi, S., Derakhshani, A., Mohammadi, M.A., Mousavi, S.M., Baneshi, M.R., Hiby, E., and Harandi, M.F. (2022). Dynamic modeling of female neutering interventions for free-roaming dog population management in an urban setting of southeastern Iran. Sci. Rep., 12.10.1038/s41598-022-08697-w ↗
7. Finding the missing link between landscape structure and population dynamics: A spatially explicit perspective10.1086/303272 ↗
8. Simulating the consequences of roads for wildlife population dynamics10.1016/j.landurbplan.2019.103672 ↗
9. Approaches to end-to-end ecosystem models10.1016/j.jmarsys.2009.12.012 ↗
10. Gephi: An open source software for exploring and manipulating networks10.1609/icwsm.v3i1.13937 ↗
11. Understanding models with Vensim™10.1016/0377-2217(92)90018-5 ↗
12. Borshchev, A. (2014). Multi-method modelling: AnyLogic. Discrete-Event Simulation and System Dynamics for Management Decision Making, John Wiley & Sons.10.1002/9781118762745.ch12 ↗
13. NetLogo: A simple environment for modeling complexity
14. Grignard, A., Taillandier, P., Gaudou, B., Vo, D.A., Huynh, N.Q., and Drogoul, A. (2013, January 1–6). GAMA 1.6: Advancing the art of complex agent-based modeling and simulation. Proceedings of the PRIMA 2013: Principles and Practice of Multi-Agent Systems: 16th International Conference, Dunedin, New Zealand.10.1007/978-3-642-44927-7_9 ↗
15. Repast: An extensible framework for agent simulation
16. Mason: A multiagent simulation environment10.1177/0037549705058073 ↗
17. Minar, N., Burkhart, R., Langton, C., and Askenazi, M. (1996). The Swarm Simulation System: A Toolkit for Building Multi-Agent Simulations, Santa Fe Institute. SFI Working Paper 1996-06-042.
18. Stubben, C., and Milligan, B. (2007). popbio: Construction and analysis of matrix population models. R Package, version 2.8, R Project.
19. WiSP: A web-based interactive simulation program for population dynamics
20. Conroy, M.J., and Carroll, J.P. (2011). A Guide to Wildlife Radio Tracking, Springer Science & Business Media.
21. Troubling trends in scientific software use10.1126/science.1231535 ↗
22. Marru, S., Gunathilake, L., Herath, C., Tangchaisin, P., Pierce, M., Mattmann, C., Singh, R., Gunarathne, T., Chinthaka, E., and Gardler, R. (2011, January 18). Apache airavata: A framework for distributed applications and computational workflows. Proceedings of the 2011 ACM Workshop on Gateway Computing Environments, Seattle, WA, USA.10.1145/2110486.2110490 ↗
23. Decker, D.J., Riley, S.J., and Siemer, W.F. (2012). Human Dimensions of Wildlife Management, JHU Press.10.56021/9781421406541 ↗
24. Evolution of co-management: Role of knowledge generation, bridging organizations and social learning10.1016/j.jenvman.2008.12.001 ↗
25. Testing disturbance theory with long-term data: Alternative life-history solutions to the distribution of events10.1086/285967 ↗
26. Notice sur la loi que la population suit dans son accroissement
27. Random walk models in biology10.1098/rsif.2008.0014 ↗
28. Analyzing insect movement as a correlated random walk10.1007/BF00379695 ↗
29. Cellular automata as a paradigm for ecological modeling
30. Fitzpatrick, M. (2021). Create GUI Applications with Python & Qt6 (PySide6 Edition), Martin Fitzpatrick.
31. Masad, D., and Kazil, J.L. (2015, January 6–12). Mesa: An Agent-Based Modeling Framework. Proceedings of the SciPy, Austin, TX, USA.10.25080/Majora-7b98e3ed-009 ↗
32. Pattern-oriented modeling of agent-based complex systems: Lessons from ecology10.1126/science.1116681 ↗
33. Pytorch: An imperative style, high-performance deep learning library
34. Kramer, O. (2016). Scikit-learn. Machine Learning for Evolution Strategies, Springer.10.1007/978-3-319-33383-0 ↗
35. Dynamic programming10.1126/science.153.3731.34 ↗
36. Planning and acting in partially observable stochastic domains10.1016/S0004-3702(98)00023-X ↗
37. Laplace, P.S. (1820). Théorie Analytique des Probabilités, Courcier.
38. Impact of extreme weather events and climate change for health and social care systems10.1186/s12940-017-0324-3 ↗
39. Climate extremes and the carbon cycle10.1038/nature12350 ↗
40. Statistical methods for the analysis of climate extremes10.1016/j.crte.2005.04.015 ↗
41. UK Office for National Statistics, and Department for Environment, Food & Rural Affairs (2024, December 01). Smoothed [Dataset], Available online: https://www.gov.uk/government/statistics/butterflies-in-the-wider-countryside-uk.