Evaluating Bayesian spatial methods for modelling species distributions with clumped and restricted occurrence data

Statistical approaches for inferring the spatial distribution of taxa (Species Distribution Models, SDMs) commonly rely on available occurrence data, which is often clumped and geographically restricted. Although available SDM methods address some of these factors, they could be more directly and accurately modelled using a spatially-explicit approach. Software to fit models with spatial autocorrelation parameters in SDMs are now widely available, but whether such approaches for inferring SDMs aid predictions compared to other methodologies is unknown. Here, within a simulated environment using 1000 generated species’ ranges, we compared the performance of two commonly used non-spatial SDM methods (Maximum Entropy Modelling, MAXENT and boosted regression trees, BRT), to a spatial Bayesian SDM method (fitted using R-INLA), when the underlying data exhibit varying combinations of clumping and geographic restriction. Finally, we tested how any recommended methodological settings designed to account for spatially non-random patterns in the data impact inference. Spatial Bayesian SDM method was the most consistently accurate method, being in the top 2 most accurate methods in 7 out of 8 data sampling scenarios. Within high-coverage sample datasets, all methods performed fairly similarly. When sampling points were randomly spread, BRT had a 1–3% greater accuracy over the other methods and when samples were clumped, the spatial Bayesian SDM method had a 4%-8% better AUC score. Alternatively, when sampling points were restricted to a small section of the true range all methods were on average 10–12% less accurate, with greater variation among the methods. Model inference under the recommended settings to account for autocorrelation was not impacted by clumping or restriction of data, except for the complexity of the spatial regression term in the spatial Bayesian model. Methods, such as those made available by R-INLA, can be successfully used to account for spatial autocorrelation in an SDM context and, by taking account of random effects, produce outputs that can better elucidate the role of covariates in predicting species occurrence. Given that it is often unclear what the drivers are behind data clumping in an empirical occurrence dataset, or indeed how geographically restricted these data are, spatially-explicit Bayesian SDMs may be the better choice when modelling the spatial distribution of target species

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doi:10.1186/1757-7241-16

The role of population structure and size in determining bat pathogen richness

Pathogens acquired from animals make up the majority of emerging human diseases, are often highly virulent and can have large effects on public health and economic development. Identifying species with high pathogen species richness enables efficient sampling and monitoring of potentially dangerous pathogens. I examine the role of host population structure and size in maintaining pathogen species richness in an important reservoir host for zoonotic viruses, bats (Order, Chiroptera). Firstly I test whether population structure is associated with high viral richness across bat species with a comparative, phylogenetic analysis. I find evidence that bat species with more structured populations have more virus species. As this type of study cannot distinguish between specific mechanisms, I then formulate epidemiological models to test whether more structured host populations may allow invading pathogens to avoid competition. However, these models show that increasing population structure decreases the rate of pathogen invasion. As both global host population structure and local group size appear to be important for disease invasion, I use the same modelling framework to compare the importance of host density, group size and number of groups. I find that host group size has a stronger effect than density or number of groups. There are few bat population size estimates to empirically test the importance of host population size on pathogen richness. Therefore, to assist future research, I develop a method for estimating bat population sizes from acoustic surveys. Overall in this thesis, I show that the structure and size of host bat populations can affect their ability to maintain many pathogen species and I provide a method to measure population sizes of bats. These findings increase our understanding of the ecological process of pathogen community construction and can help optimise surveillance for zoonotic pathogens

The Utstein template for uniform reporting of data following major trauma: A joint revision by SCANTEM, TARN, DGU-TR and RITG

<p>Abstract</p> <p>Background</p> <p>In 1999, an Utstein Template for Uniform Reporting of Data following Major Trauma was published. Few papers have since been published based on that template, reflecting a lack of international consensus on its feasibility and use. The aim of the present revision was to further develop the Utstein Template, particularly with a major reduction in the number of core data variables and the addition of more precise definitions of data variables. In addition, we wanted to define a set of inclusion and exclusion criteria that will facilitate uniform comparison of trauma cases.</p> <p>Methods</p> <p>Over a ten-month period, selected experts from major European trauma registries and organisations carried out an Utstein consensus process based on a modified nominal group technique.</p> <p>Results</p> <p>The expert panel concluded that a New Injury Severity Score > 15 should be used as a single inclusion criterion, and five exclusion criteria were also selected. Thirty-five precisely defined core data variables were agreed upon, with further division into core data for Predictive models, System Characteristic Descriptors and for Process Mapping.</p> <p>Conclusion</p> <p>Through a structured consensus process, the Utstein Template for Uniform Reporting of Data following Major Trauma has been revised. This revision will enhance national and international comparisons of trauma systems, and will form the basis for improved prediction models in trauma care.</p

Responsible modelling: Unit testing for infectious disease epidemiology

Infectious disease epidemiology is increasingly reliant on large-scale computation and inference. Models have guided health policy for epidemics including COVID-19 and Ebola and endemic diseases including malaria and tuberculosis. Yet a coding bug may bias results, yielding incorrect conclusions and actions causing avoidable harm. We are ethically obliged to make our code as free of error as possible. Unit testing is a coding method to avoid such bugs, but it is rarely used in epidemiology. We demonstrate how unit testing can handle the particular quirks of infectious disease models and aim to increase the uptake of this methodology in our field

Responsible modelling: Unit testing for infectious disease epidemiology

Infectious disease epidemiology is increasingly reliant on large-scale computation and inference. Models have guided health policy for epidemics including COVID-19 and Ebola and endemic diseases including malaria and tuberculosis. Yet a coding bug may bias results, yielding incorrect conclusions and actions causing avoidable harm. We are ethically obliged to make our code as free of error as possible. Unit testing is a coding method to avoid such bugs, but it is rarely used in epidemiology. We demonstrate how unit testing can handle the particular quirks of infectious disease models and aim to increase the uptake of this methodology in our field

A generalised random encounter model for estimating animal density with remote sensor data

Summary: Wildlife monitoring technology is advancing rapidly and the use of remote sensors such as camera traps and acoustic detectors is becoming common in both the terrestrial and marine environments. Current methods to estimate abundance or density require individual recognition of animals or knowing the distance of the animal from the sensor, which is often difficult. A method without these requirements, the random encounter model (REM), has been successfully applied to estimate animal densities from count data generated from camera traps. However, count data from acoustic detectors do not fit the assumptions of the REM due to the directionality of animal signals. We developed a generalised REM (gREM), to estimate absolute animal density from count data from both camera traps and acoustic detectors. We derived the gREM for different combinations of sensor detection widths and animal signal widths (a measure of directionality). We tested the accuracy and precision of this model using simulations of different combinations of sensor detection widths and animal signal widths, number of captures and models of animal movement. We find that the gREM produces accurate estimates of absolute animal density for all combinations of sensor detection widths and animal signal widths. However, larger sensor detection and animal signal widths were found to be more precise. While the model is accurate for all capture efforts tested, the precision of the estimate increases with the number of captures. We found no effect of different animal movement models on the accuracy and precision of the gREM. We conclude that the gREM provides an effective method to estimate absolute animal densities from remote sensor count data over a range of sensor and animal signal widths. The gREM is applicable for count data obtained in both marine and terrestrial environments, visually or acoustically (e.g. big cats, sharks, birds, echolocating bats and cetaceans). As sensors such as camera traps and acoustic detectors become more ubiquitous, the gREM will be increasingly useful for monitoring unmarked animal populations across broad spatial, temporal and taxonomic scales