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1. Patches as an expressive medium for exploratory multi‐agent modelling

   https://doi.org/10.1111/bjet.13087  

   Brady, Corey (April 2021, British Journal of Educational Technology)

   Abstract This paper outlines the potential gains for Constructionist research and praxis in modelling that might be obtained by recognising the power of the Patch—a humble computational being in the NetLogo modelling environment that has been overshadowed by its more popular fellow agent, the Turtle. To contextualise this opportunity, I describe how Constructionist modelling has thrived by promoting forms of learning that rely on learners’ identifying with agents. I argue that patches are a neglected agent type in this multi‐agent modelling tradition, and that the possibilities for learners to adopt the patch perspective in support of exploratory forms of modelling and aesthetic expression have been under‐researched. Nevertheless, I show there are a variety of powerful ways for learners––both individually and in groups––to identify with patches. I describe ongoing research showing how taking an aesthetic approach to patches has the potential to support individuals and groups in powerful forms of learning with and about multi‐agent modelling. Practitioner notesWhat is already known about this topicTurtles (movable agents in Logo and Constructionist environments descended from Logo) can be ‘transitional objects’ that provide learners a way to make powerful ideas their own.These agents can be powerful ‘objects‐to‐think‐with’ in large part because they encourage learners to identify with them in a form of learning known as ‘syntonic learning’.Expressive activities that draw on learners’aestheticinterests can support their learning with and about computational representations.Multi‐agent modelling is a powerful extension of Logo‐based learning environments that provides access to powerful ideas about complex systems and their emergent properties.In the multi‐agent setting, individual learners and/or groups of learners can identify syntonically with agents to provide entry points for reasoning about complexity.What this paper addsPatches (non‐movable agents in the NetLogo modelling environment) are under‐represented in the research on multi‐agent modelling, and the potential for learners to adopt the patches’ perspective has been neglected.An aesthetically driven approach to patches can ground students’ understanding of their expressive value.Participatory activities in which learners play the role of patches (called ‘Stadium Card’ activities) can ground the patch perspective, so that learners can achieve a form of syntonicity and/or collectively adopt the perspective of patches in the aggregate.Participatory activities that blend intrinsic and extrinsic perspectives on the patch grid can further enhance learners’ facility with programming for patches and their understanding of patches’ collective expressive power.Implications for practice and/or policyBalancing the focus between turtles and patches can enrich the modelling toolbox of learners new to agent‐based modelling.Patchesdocapture important aspects of individual and collective experience, and so can be good objects‐to‐think‐with, especially when conceptualising phenomena at a larger scale.The expressive potential of the patch grid is an important topic for computer science as well (eg, through 2D cellular automata). This is a rich context for learning in itself, which can be made accessible to groups of learners through physical or virtual participatory role‐play.Moreover, physical or virtual grids of people‐patches may exhibit novel aggregate computational properties that could in turn become interesting areas for research in computer science. 

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2. The transition from resistance to acceptance: Managing a marine invasive species in a changing world

   https://doi.org/10.1111/1365-2664.14881  

   Keller, Abigail_G; Counihan, Timothy_D; Grosholz, Edwin_D; Boettiger, Carl (January 2025, Journal of Applied Ecology)

   Abstract Marine invasive species can transform coastal ecosystems, yet mitigating their effects can be difficult, and even impractical. Often, marine invasive species are managed at poorly matched spatial scales, and at the same time, rates of spread and establishment are increasing under climate change and can outpace resources available for population suppression. These circumstances challenge traditional conservation goals of maintaining a historic environmental state, especially for a species like the European green crab (Carcinus maenas), a formidable invader with few examples of successful long‐term removal programs.A management paradigm where decision alternatives include resisting or accepting a new ecological trajectory may be needed. We apply mathematical concepts from decision theory to develop a quantitative framework for navigating management decisions in this new resist‐accept paradigm. We develop a model of European green crab growth, removal and colonization, and we find optimal levels of removal effort that minimize both ecological change and removal cost.We establish a benchmark of colonization pressure at which green crab density becomes decoupled from a decision maker's actions, such that population control can no longer shape the invasion trajectory. For informing the decision boundary between resistance and acceptance, our results highlight that a decision maker's understanding of how removal cost scales with removal effort is more important than understanding the density‐impact relationship.We show that assuming stationary system dynamics can result in sub‐optimal levels of species removal effort, highlighting the importance of developing anticipatory management strategies by accounting for non‐stationary dynamics.Policy implications. For marine invasive species that can disperse across long distances and recolonize rapidly after removal, the focus of conservation policy should shift away from understandinghowto resist change to understandingwhen to stopresisting change. Navigating this decision problem involves trade‐offs among competing objectives, highlighting the need for structured approaches to elicit objective weights that reflect the values of the decision maker. For natural resource managers facing possible ecosystem transformation, this decision framework can enable proactive and strategic decisions made under uncertainty in a changing world. 

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3. Migration and tolerance shape host behaviour and response to parasite infection

   https://doi.org/10.1111/1365-2656.13539  

   Kim, Dongmin; Shaw, Allison K. (June 2021, Journal of Animal Ecology)

   Abstract Numerous theoretical models have demonstrated that migration, a seasonal animal movement behaviour, can minimize the risks and costs of parasite infection. Past work on migration–infection interactions assumes migration is the only strategy available to organisms for dealing with the parasite infection, that is they migrate to a different environment to recover or escape from infection. Thus, migration is similar to the non‐spatial strategy of resistance, where hosts prevent infection or kill parasites once infected. However, an alternative defence strategy is to tolerate the infection and experience a lower cost to the infection. To our knowledge, no studies have examined how migration can change based on combining two host strategies (migration and tolerance) for dealing with parasites.In this paper, we aim to understand how both parasite transmission and infection tolerance can influence the host's migratory behaviour.We constructed a model that incorporates two host strategies (migration and tolerance) to understand whether allowing for tolerance affects the proportion of the population that migrates at equilibrium in response to infection.We show that the benefits of tolerance can either decrease or increase the host's migration. Also, if the benefit of migration is great, then individuals are more likely to migrate regardless of the presence of tolerance. Finally, we find that the transmission rate of parasite infection can either decrease or increase the tolerant host's migration, depending on the cost of migration.These findings highlight that adopting two defence strategies is not always beneficial to the hosts. Instead, a single strategy is often better, depending on the costs and benefits of the strategies and infection pressures. Our work further suggests that multiple host‐defence strategies as a potential explanation for the evolution of migration to minimize the parasite infection. Moreover, migration can also affect the ecological and evolutionary dynamics of parasite–host interactions. 

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4. On the Allee effect and directed movement on the whole space

   https://doi.org/10.3934/mbe.2023347  

   Cosner, Chris; Rodríguez, Nancy (January 2023, Mathematical Biosciences and Engineering)

   It is well known that relocation strategies in ecology can make the difference between extinction and persistence. We consider a reaction-advection-diffusion framework to analyze movement strategies in the context of species which are subject to a strong Allee effect. The movement strategies we consider are a combination of random Brownian motion and directed movement through the use of an environmental signal. We prove that a population can overcome the strong Allee effect when the signals are super-harmonic. In other words, an initially small population can survive in the long term if they aggregate sufficiently fast. A sharp result is provided for a specific signal that can be related to the Fokker-Planck equation for the Orstein-Uhlenbeck process. We also explore the case of pure diffusion and pure aggregation and discuss their benefits and drawbacks, making the case for a suitable combination of the two as a better strategy. 

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5. NAPS : Integrating pose estimation and tag‐based tracking

   https://doi.org/10.1111/2041-210X.14201  

   Wolf, Scott W.; Ruttenberg, Dee M.; Knapp, Daniel Y.; Webb, Andrew E.; Traniello, Ian M.; McKenzie‐Smith, Grace C.; Leheny, Sophie A.; Shaevitz, Joshua W.; Kocher, Sarah D. (August 2023, Methods in Ecology and Evolution)

   Abstract Significant advances in computational ethology have allowed the quantification of behaviour in unprecedented detail. Tracking animals in social groups, however, remains challenging as most existing methods can either capture pose or robustly retain individual identity over time but not both.To capture finely resolved behaviours while maintaining individual identity, we built NAPS (NAPS is ArUco Plus SLEAP), a hybrid tracking framework that combines state‐of‐the‐art, deep learning‐based methods for pose estimation (SLEAP) with unique markers for identity persistence (ArUco). We show that this framework allows the exploration of the social dynamics of the common eastern bumblebee (Bombus impatiens).We provide a stand‐alone Python package for implementing this framework along with detailed documentation to allow for easy utilization and expansion. We show that NAPS can scale to long timescale experiments at a high frame rate and that it enables the investigation of detailed behavioural variation within individuals in a group.Expanding the toolkit for capturing the constituent behaviours of social groups is essential for understanding the structure and dynamics of social networks. NAPS provides a key tool for capturing these behaviours and can provide critical data for understanding how individual variation influences collective dynamics. 

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