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Data from: A generalized residual technique for analyzing complex movement models using earth mover's distance
Potts, Jonathan R.; Auger-Méthé, Marie; Mokross, Karl; Lewis, Mark A. — 2015-08-18 1. Complex systems of moving and interacting objects are ubiquitous in the natural and social sciences. Predicting their behavior often requires models that mimic these systems with sufficient accuracy, while accounting for their inherent stochasticity. Though tools exist to determine which of a set of candidate models is best relative to the others, there is currently no generic goodness-of-fit framework for testing how close the best model is to the real complex stochastic system. 2. We propose such a framework, using a novel application of the Earth mover's distance, also known as the Wasserstein metric. It is applicable to any stochastic process where the probability of the model's state at time t is a function of the state at previous times. It generalizes the concept of a residual, often used to analyze 1D summary statistics, to situations where the complexity of the underlying model's probability distribution makes standard residual analysis too imprecise for practical use. 3. We give a scheme for testing the hypothesis that a model is an accurate description of a data set. We demonstrate the tractability and usefulness of our approach by application to animal movement models in complex, heterogeneous environments. We detail methods for visualizing results and extracting a variety of information on a given model's quality, such as whether there is any inherent bias in the model, or in which situations it is most accurate. We demonstrate our techniques by application to data on multi-species flocks of insectivore birds in the Amazon rainforest. 4. This work provides a usable toolkit to assess the quality of generic movement models of complex systems, in an absolute rather than a relative sense.
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Data from: A unifying framework for quantifying the nature of animal interactions
Potts, Jonathan R.; Mokross, Karl; Lewis, Mark A. — 2015-04-29 Collective phenomena, whereby agent-agent interactions determine spatial patterns, are ubiquitous in the animal kingdom. On the other hand, movement and space use are also greatly influenced by the interactions between animals and their environment. Despite both types of interaction fundamentally influencing animal behaviour, there has hitherto been no unifying framework for the models proposed in both areas. Here, we construct a general method for inferring population-level spatial patterns from underlying individual movement and interaction processes, a key ingredient in building a statistical mechanics for ecological systems. We show that resource selection functions, as well as several examples of collective motion models, arise as special cases of our framework, thus bringing together resource selection analysis and collective animal behaviour into a single theory. In particular, we focus on combining the various mechanistic models of territorial interactions in the literature with step selection functions, by incorporate interactions into the step selection framework and demonstrating how to derive territorial patterns from the resulting models. We demonstrate the efficacy of our model by application to a population of insectivore birds in the Amazon rainforest.
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Data from: Aggregation and a strong Allee effect in a cooperative outbreak insect
Goodsman, Devin W.; Koch, Dean; Whitehouse, Caroline; Evenden, Maya L.; Cooke, Barry J.; Lewis, Mark A. — 2016-06-20 Most species that are negatively impacted when their densities are low aggregate to minimize this effect. Aggregation has the potential to change how Allee effects are expressed at the population level. We studied the interplay between aggregation and Allee effects in the mountain pine beetle (Dendroctonus ponderosae Hopkins), an irruptive bark beetle that aggregates to overcome tree defenses. By cooperating to surpass a critical number of attacks per tree, the mountain pine beetle is able to breach host defenses,oviposit and reproduce. Mountain pine beetles and Hymenopteran parasitoids share some biological features, the most notable of which is obligatory host death as a consequence of parasitoid attack and development. We developed spatiotemporal models of mountain pine beetle dynamics that were based on the Nicholson-Bailey framework but which featured beetle aggregation and a tree-level attack threshold. By fitting our models to data from a local mountain pine beetle outbreak, we demonstrate that due to aggregation, attack thresholds at the tree level can be overcome by a surprisingly low ratio of beetles per susceptible tree at the stand level. This results confirms the importance of considering aggregation in models of organisms that are subject to strong Allee effects.
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Data from: Predicting local and non-local effects of resources on animal space use using a mechanistic step-selection model
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Potts, Jonathan R.; Bastille-Rousseau, Guillaume; Murray, Dennis L.; Schaefer, James A.; Lewis, Mark A. — 2014-11-19 1. Predicting space use patterns of animals from their interactions with the environment is fundamental for understanding the effect of habitat changes on ecosystem functioning. Recent attempts to address this problem have sought to unify resource selection analysis, where animal space use is derived from available habitat quality, and mechanistic movement models, where detailed movement processes of an animal are used to predict its emergent utilisation distribution. Such models bias the animal's movement towards patches that are easily available and resource-rich, and the result is a predicted probability density at a given position being a function of the habitat quality at that position. However, in reality, the probability that an animal will use a patch of the terrain tends to be a function of the resource quality in both that patch and the surrounding habitat. 2. We propose a mechanistic model where this non-local effect of resources naturally emerges from the local movement processes, by taking into account the relative utility of both the habitat where the animal currently resides and that of where it is moving. We give statistical techniques to parametrize the model from location data, and demonstrate application of these techniques to GPS location data of caribou (Rangifer tarandus) in Newfoundland. 3. Steady-state animal probability distributions arising from the model have complex patterns that cannot be expressed simply as a function of the local quality of the habitat. In particular, large areas of good habitat are used more intensively than smaller patches of equal quality habitat, whereas isolated patches are used less frequently. Both of these are real aspects of animal space use missing from previous mechanistic resource-selection models. 4. Whilst we focus on habitats in this paper, our modelling framework can be readily used with any environmental covariates, and therefore represents a unification of mechanistic modelling and step-selection approaches to understanding animal space use.
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Data from: Next-generation matrices for marine metapopulations: the case of sea lice and salmon farms
Harrington, Peter D.; Cantrell, Danielle L.; Lewis, Mark A. — 2023-04-19 <p>Classifying habitat patches as sources or sinks and determining metapopulation persistence requires coupling connectivity between habitat patches with local demographic rates.  While methods to calculate sources, sinks, and metapopulation persistence exist for discrete-time models, there is no method that is consistent across modelling frameworks. In this paper, we show how next-generation matrices, originally popularized in epidemiology to calculate new infections after one generation, can be used in an ecological context to calculate sources and sinks as well as metapopulation persistence in marine metapopulations. To demonstrate the utility of the method, we construct a next-generation matrix for a network of sea lice populations on salmon farms in the Broughton Archipelago, BC, an intensive salmon farming region on the west coast of Canada where certain salmon farms are currently being removed under an agreement between local First Nations and the provincial government. The column sums of the next-generation matrix can determine if a habitat patch is a source or a sink and the spectral radius of the next-generation matrix can determine the persistence of the metapopulation. With respect to salmon farms in the Broughton Archipelago, we identify the salmon farms which are acting as the largest sources of sea lice and show that in this region, the most productive sea lice populations are also the most connected. The farms which are the largest sources of sea lice have not yet been removed from the Broughton Archipelago, and warming temperatures could lead to increased sea louse growth. Calculating sources, sinks and persistence in marine metapopulations using the next-generation matrix is biologically intuitive, mathematically equivalent to previous methods, and consistent across different modelling frameworks.</p>
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Data from: Evidence-based tool surpasses expert opinion in predicting probability of eradication of aquatic nonindigenous species
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Drolet, David; Locke, Andrea; Lewis, Mark A.; Davidson, Jeff — 2015-08-07 The main objective of evidence-based management is to promote use of scientific data in the decision-making process of managers, with data either complementing or replacing expert knowledge. It is expected that this will increase the efficiency of environmental interventions. However, the relative accuracy and precision of evidence-based tools and expert knowledge has seldom been evaluated. It is therefore essential to verify whether such tools provide better decision support before advocating their use. We conducted an elicitation survey in which experts were asked to (1) evaluate the influence of various factors on the success of eradication programs for aquatic nonindigenous species and (2) provide probabilities of success for real case studies for which we knew the outcome. The responses of experts were compared with the results and predictions of a newly developed evidence-based tool: a statistical model calibrated with a meta-analysis of case studies designed to evaluate probability of eradication. Experts and the model generally identified the same factors as influencing the probability of success. However, the model provided much more accurate estimates for the probability of eradication than expert opinion, strongly suggesting that an evidence-based approach is superior to expert knowledge in this case. Uncertainty surrounding the predictions of the evidence-based tool was similar to among-expert variability. Finally, a model based on ≥30 case studies returned more accurate predictions than expert opinion. We conclude that decision-making processes based on expert judgment would greatly benefit from incorporating evidence-based tools.
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Data from: Timing and probability of arrival for sea lice dispersing between salmon farms
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Harrington, Peter D.; Cantrell, Danielle L.; Foreman, Michael G. G.; Guo, Ming; Lewis, Mark A. — 2023-01-11 <p>Sea lice are a threat to the health of both wild and farmed salmon and an economic burden for salmon farms. With a free-living larval stage, sea lice can disperse tens of kilometers in the ocean between salmon farms, leading to connected sea lice populations that are difficult to control in isolation. In this paper, we develop a simple analytical model for the dispersal of sea lice between two salmon farms. From the model we calculate the arrival time distribution of sea lice dispersing between farms, as well as the level of cross-infection of sea lice. We also use numerical flows from a hydrodynamic model, coupled with a particle tracking model, to directly calculate the arrival time of sea lice dispersing between two farms in the Broughton Archipelago, BC, in order to fit our analytical model and find realistic parameter estimates. Using the parametrized analytical model we show that there is often an intermediate inter-farm spacing that maximizes the level of cross-infection between farms, and that increased temperatures will lead to increased levels of cross-infection.</p>
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Dataset of mountain pine beetle outbreak dynamics and direct control in Cypress Hills, SK
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Kunegel-Lion, Mélodie; McIntosh, Rory L.; Lewis, Mark A. — 2020-02-26 <p>The data presented in this article are related to the research article entitled “Mountain pine beetle outbreak duration and pine mortality depend on direct control effort” [1]. This article provides presence of mountain pine beetle infested trees detected by the Saskatchewan Forest Service on a grid covering the spatial extent of the Saskatchewan portion of the Cypress Hills interprovincial park between 2006 and 2018. For each grid cell, associated ecological and environmental covariates, such as topography, weather and vegetation, are also provided. These data cover the spatio-temporal extent of an almost entire mountain pine beetle outbreak and contribute to the understanding of mountain pine beetle outbreak dynamics.</p> <p> </p>
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Codes and data for the article 'Early warning signal for river-borne diseases with almost no data'
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Ramazi, Pouria; Bende, Prajwal; Arezoo, Haratian; Greiner, Russell; Lewis, Mark A. — 2024-08-28 Codes and data for the paper "Early warning signal for river-borne diseases with almost no data". This collection includes data on the prevalence of river-borne diseases and related environmental variables.The codes are for extracting the tree structure of the river from the map and using the extended HMM model to predict the presence of contaminated samples in each part of the river. https://creativecommons.org/licenses/by/4.0/legalcode

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(Author: Lewis, Mark A.)

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