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Ribeiro R, Matthiopoulos J, Lindgren F, Tello C, Zariquiey CM, Valderrama W, Rocke TE, Streicker DG. Incorporating environmental heterogeneity and observation effort to predict host distribution and viral spillover from a bat reservoir. Proc Biol Sci 2023; 290:20231739. [PMID: 37989240 PMCID: PMC10688441 DOI: 10.1098/rspb.2023.1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Predicting the spatial occurrence of wildlife is a major challenge for ecology and management. In Latin America, limited knowledge of the number and locations of vampire bat roosts precludes informed allocation of measures intended to prevent rabies spillover to humans and livestock. We inferred the spatial distribution of vampire bat roosts while accounting for observation effort and environmental effects by fitting a log Gaussian Cox process model to the locations of 563 roosts in three regions of Peru. Our model explained 45% of the variance in the observed roost distribution and identified environmental drivers of roost establishment. When correcting for uneven observation effort, our model estimated a total of 2340 roosts, indicating that undetected roosts (76%) exceed known roosts (24%) by threefold. Predicted hotspots of undetected roosts in rabies-free areas revealed high-risk areas for future viral incursions. Using the predicted roost distribution to inform a spatial model of rabies spillover to livestock identified areas with disproportionate underreporting and indicated a higher rabies burden than previously recognized. We provide a transferrable approach to infer the distribution of a mostly unobserved bat reservoir that can inform strategies to prevent the re-emergence of an important zoonosis.
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Affiliation(s)
- Rita Ribeiro
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Graham Kerr Building, Glasgow G12 8QQ, UK
| | - Jason Matthiopoulos
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Graham Kerr Building, Glasgow G12 8QQ, UK
| | - Finn Lindgren
- School of Mathematics, University of Edinburgh, Edinburgh, UK
| | - Carlos Tello
- ILLARIY (Asociación para el Desarrollo y Conservación de los Recursos Naturales), Lima, Perú
- Yunkawasi, Lima, Perú
| | - Carlos M. Zariquiey
- ILLARIY (Asociación para el Desarrollo y Conservación de los Recursos Naturales), Lima, Perú
| | - William Valderrama
- ILLARIY (Asociación para el Desarrollo y Conservación de los Recursos Naturales), Lima, Perú
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Tonie E. Rocke
- National Wildlife Health Center, US Geological Survey, Madison, Wisconsin, USA
| | - Daniel G. Streicker
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, University Avenue, Graham Kerr Building, Glasgow G12 8QQ, UK
- Medical Research Council—University of Glasgow Centre for Virus Research, Glasgow, UK
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2
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Schirmer S, Korner-Nievergelt F, von Rönn JAC, Liebscher V. Estimating survival in continuous space from mark-dead-recovery data - Towards a continuous version of the multinomial dead recovery model. J Theor Biol 2023; 574:111625. [PMID: 37748534 DOI: 10.1016/j.jtbi.2023.111625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/15/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Understanding spatially varying survival is crucial for understanding the ecology and evolution of migratory animals, which may ultimately help to conserve such species. We develop an approach to estimate an annual survival probability function varying continuously in geographic space, if the recovery probability is constant over space. This estimate is based on a density function over continuous geographic space and the discrete age at death obtained from dead recovery data. From the same density function, we obtain an estimate for animal distribution in space corrected for survival, i.e., migratory connectivity. This is possible, when migratory connectivity can be separated from recovery probability. In this article, we present the method how spatially and continuously varying survival and the migratory connectivity corrected for survival can be obtained, if a constant recovery probability can be assumed reasonably. The model is a stepping stone in developing a model allowing for disentangling spatially heterogeneous survival and migratory connectivity corrected for survival from a spatially heterogeneous recovery probability. We implement the method using kernel density estimates in the R-package CONSURE. Any other density estimation technique can be used as an alternative. In a simulation study, the estimators are unbiased but show edge effects in survival and migratory connectivity. Applying the method to a real-world data set of European robins Erithacus rubecula results in biologically reasonable continuous heat-maps for survival and migratory connectivity.
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Affiliation(s)
- Saskia Schirmer
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17489 Greifswald, Germany; Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland; Zoological Institute and Museum, University of Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany.
| | | | - Jan A C von Rönn
- Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland
| | - Volkmar Liebscher
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17489 Greifswald, Germany
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3
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Zhang W, Chipperfield JD, Illian JB, Dupont P, Milleret C, de Valpine P, Bischof R. A flexible and efficient Bayesian implementation of point process models for spatial capture-recapture data. Ecology 2023; 104:e3887. [PMID: 36217822 PMCID: PMC10078592 DOI: 10.1002/ecy.3887] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 07/29/2022] [Accepted: 08/29/2022] [Indexed: 02/01/2023]
Abstract
Spatial capture-recapture (SCR) is now routinely used for estimating abundance and density of wildlife populations. A standard SCR model includes sub-models for the distribution of individual activity centers (ACs) and for individual detections conditional on the locations of these ACs. Both sub-models can be expressed as point processes taking place in continuous space, but there is a lack of accessible and efficient tools to fit such models in a Bayesian paradigm. Here, we describe a set of custom functions and distributions to achieve this. Our work allows for more efficient model fitting with spatial covariates on population density, offers the option to fit SCR models using the semi-complete data likelihood (SCDL) approach instead of data augmentation, and better reflects the spatially continuous detection process in SCR studies that use area searches. In addition, the SCDL approach is more efficient than data augmentation for simple SCR models while losing its advantages for more complicated models that account for spatial variation in either population density or detection. We present the model formulation, test it with simulations, quantify computational efficiency gains, and conclude with a real-life example using non-invasive genetic sampling data for an elusive large carnivore, the wolverine (Gulo gulo) in Norway.
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Affiliation(s)
- Wei Zhang
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA.,School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - Joseph D Chipperfield
- Faculty of Life Sciences and Natural Resource Management, Norwegian University of Life Sciences, Trondheim, Norway.,Norwegian Institute for Nature Research, Høyteknologisenteret, Bergen, Norway
| | - Janine B Illian
- School of Mathematics and Statistics, University of Glasgow, Glasgow, UK
| | - Pierre Dupont
- Faculty of Life Sciences and Natural Resource Management, Norwegian University of Life Sciences, Trondheim, Norway
| | - Cyril Milleret
- Faculty of Life Sciences and Natural Resource Management, Norwegian University of Life Sciences, Trondheim, Norway
| | - Perry de Valpine
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Richard Bischof
- Faculty of Life Sciences and Natural Resource Management, Norwegian University of Life Sciences, Trondheim, Norway
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4
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Arnone E, Ferraccioli F, Pigolotti C, Sangalli LM. A roughness penalty approach to estimate densities over two-dimensional manifolds. Comput Stat Data Anal 2022. [DOI: 10.1016/j.csda.2022.107527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Chiuchiolo C, van Niekerk J, Rue H. Joint posterior inference for latent Gaussian models with R-INLA. J STAT COMPUT SIM 2022. [DOI: 10.1080/00949655.2022.2117813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Cristian Chiuchiolo
- CEMSE Division, Department of Statistics, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Janet van Niekerk
- CEMSE Division, Department of Statistics, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Håvard Rue
- CEMSE Division, Department of Statistics, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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6
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Comparing distribution of harbour porpoise using generalized additive models and hierarchical Bayesian models with integrated nested laplace approximation. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Schmidt JH, Thompson WL, Wilson TL, Reynolds JH. Distance sampling surveys: using components of detection and total error to select among approaches. WILDLIFE MONOGRAPHS 2022. [DOI: 10.1002/wmon.1070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Joshua H. Schmidt
- U.S. National Park Service Central Alaska Network 4175 Geist Road Fairbanks AK 99709 USA
| | | | - Tammy L. Wilson
- U.S. National Park Service, Southwest Alaska Network 240 W. 5th Avenue Anchorage AK 99501 USA
| | - Joel H. Reynolds
- U.S. National Park Service 240 W. 5th Avenue Anchorage AK 99501 USA
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8
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Flagg K, Hoegh A. The integrated nested Laplace approximation applied to spatial log-Gaussian Cox process models. J Appl Stat 2022; 50:1128-1151. [PMID: 37009597 PMCID: PMC10062232 DOI: 10.1080/02664763.2021.2023116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Spatial point process models are theoretically useful for mapping discrete events, such as plant or animal presence, across space; however, the computational complexity of fitting these models is often a barrier to their practical use. The log-Gaussian Cox process (LGCP) is a point process driven by a latent Gaussian field, and recent advances have made it possible to fit Bayesian LGCP models using approximate methods that facilitate rapid computation. These advances include the integrated nested Laplace approximation (INLA) with a stochastic partial differential equations (SPDE) approach to sparsely approximate the Gaussian field and an extension using pseudodata with a Poisson response. To help link the theoretical results to statistical practice, we provide an overview of INLA for point process data and then illustrate their implementation using freely available data. The analyzed datasets include both a completely observed spatial field and an incomplete data situation. Our well-commented R code is shared in the online supplement. Our intent is to make these methods accessible to the practitioner of spatial statistics without requiring deep knowledge of point process theory.
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Affiliation(s)
- Kenneth Flagg
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Andrew Hoegh
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
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9
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Watson J, Joy R, Tollit D, Thornton SJ, Auger-Méthé M. Estimating animal utilization distributions from multiple data types: A joint spatiotemporal point process framework. Ann Appl Stat 2021. [DOI: 10.1214/21-aoas1472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Joe Watson
- Department of Statistics, University of British Columbia
| | - Ruth Joy
- School of Environmental Science, Simon Fraser University and SMRU Consulting
| | | | | | - Marie Auger-Méthé
- Institute for the Oceans & Fisheries and the Department of Statistics, University of British Columbia
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10
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Miller DL, Fifield D, Wakefield E, Sigourney DB. Extending density surface models to include multiple and double-observer survey data. PeerJ 2021; 9:e12113. [PMID: 34557355 PMCID: PMC8418794 DOI: 10.7717/peerj.12113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/14/2021] [Indexed: 11/30/2022] Open
Abstract
Spatial models of density and abundance are widely used in both ecological research (e.g., to study habitat use) and wildlife management (e.g., for population monitoring and environmental impact assessment). Increasingly, modellers are tasked with integrating data from multiple sources, collected via different observation processes. Distance sampling is an efficient and widely used survey and analysis technique. Within this framework, observation processes are modelled via detection functions. We seek to take multiple data sources and fit them in a single spatial model. Density surface models (DSMs) are a two-stage approach: first accounting for detectability via distance sampling methods, then modelling distribution via a generalized additive model. However, current software and theory does not address the issue of multiple data sources. We extend the DSM approach to accommodate data from multiple surveys, collected via conventional distance sampling, double-observer distance sampling (used to account for incomplete detection at zero distance) and strip transects. Variance propagation ensures that uncertainty is correctly accounted for in final estimates of abundance. Methods described here are implemented in the dsm R package. We briefly analyse two datasets to illustrate these new developments. Our new methodology enables data from multiple distance sampling surveys of different types to be treated in a single spatial model, enabling more robust abundance estimation, potentially over wider geographical or temporal domains.
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Affiliation(s)
- David L Miller
- Centre for Research into Ecological and Environmental Modelling and School of Mathematics and Statistics, University of St Andrews, St Andrews, Scotland
| | - David Fifield
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Mount Pearl, NL, Canada
| | - Ewan Wakefield
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland
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11
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Ferraccioli F, Arnone E, Finos L, Ramsay JO, Sangalli LM. Nonparametric density estimation over complicated domains. J R Stat Soc Series B Stat Methodol 2021. [DOI: 10.1111/rssb.12415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Federico Ferraccioli
- Department of Statistical Sciences University of Padova Padova Veneto Italy
- MOX—Department of Mathematics Politecnico di Milano Milano Lombardia Italy
| | - Eleonora Arnone
- MOX—Department of Mathematics Politecnico di Milano Milano Lombardia Italy
| | - Livio Finos
- Department of Developmental Psychology and Socialisation University of Padova Padova Veneto Italy
| | | | - Laura M. Sangalli
- MOX—Department of Mathematics Politecnico di Milano Milano Lombardia Italy
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12
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Bravington MV, Miller DL, Hedley SL. Variance Propagation for Density Surface Models. JOURNAL OF AGRICULTURAL, BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2021. [DOI: 10.1007/s13253-021-00438-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractSpatially explicit estimates of population density, together with appropriate estimates of uncertainty, are required in many management contexts. Density surface models (DSMs) are a two-stage approach for estimating spatially varying density from distance sampling data. First, detection probabilities—perhaps depending on covariates—are estimated based on details of individual encounters; next, local densities are estimated using a GAM, by fitting local encounter rates to location and/or spatially varying covariates while allowing for the estimated detectabilities. One criticism of DSMs has been that uncertainty from the two stages is not usually propagated correctly into the final variance estimates. We show how to reformulate a DSM so that the uncertainty in detection probability from the distance sampling stage (regardless of its complexity) is captured as an extra random effect in the GAM stage. In effect, we refit an approximation to the detection function model at the same time as fitting the spatial model. This allows straightforward computation of the overall variance via exactly the same software already needed to fit the GAM. A further extension allows for spatial variation in group size, which can be an important covariate for detectability as well as directly affecting abundance. We illustrate these models using point transect survey data of Island Scrub-Jays on Santa Cruz Island, CA, and harbour porpoise from the SCANS-II line transect survey of European waters. Supplementary materials accompanying this paper appear on-line.
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13
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Perkins NR, Prall M, Chakraborty A, White JW, Baskett ML, Morgan SG. Quantifying the statistical power of monitoring programs for marine protected areas. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e2215. [PMID: 32767487 DOI: 10.1002/eap.2215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 04/15/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Marine Protected Areas (MPAs) are increasingly established globally as a spatial management tool to aid in conservation and fisheries management objectives. Assessing whether MPAs are having the desired effects on populations requires effective monitoring programs. A cornerstone of an effective monitoring program is an assessment of the statistical power of sampling designs to detect changes when they occur. We present a novel approach to power assessment that combines spatial point process models, integral projection models (IPMs) and sampling simulations to assess the power of different sample designs across a network of MPAs. We focus on the use of remotely operated vehicle (ROV) video cameras as the sampling method, though the results could be extended to other sampling methods. We use empirical data from baseline surveys of an example indicator fish species across three MPAs in California, USA as a case study. Spatial models simulated time series of spatial distributions across sites that accounted for the effects of environmental covariates, while IPMs simulated expected trends over time in abundances and sizes of fish. We tested the power of different levels of sampling effort (i.e., the number of 500-m ROV transects) and temporal replication (every 1-3 yr) to detect expected post-MPA changes in fish abundance and biomass. We found that changes in biomass are detectable earlier than changes in abundance. We also found that detectability of MPA effects was higher in sites with higher initial densities. Increasing the sampling effort had a greater effect than increasing sampling frequency on the time taken to achieve high power. High power was best achieved by combining data from multiple sites. Our approach provides a powerful tool to explore the interaction between sampling effort, spatial distributions, population dynamics, and metrics for detecting change in previously fished populations.
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Affiliation(s)
- Nicholas R Perkins
- Coastal and Marine Sciences Institute, University of California, Davis, California, 95616, USA
- California Department of Fish and Wildlife, Marine Region, Eureka, California, 95501, USA
- Institute of Marine and Antarctic Studies, University of Tasmania, Taroona, Tasmania, 7053, Australia
| | - Michael Prall
- California Department of Fish and Wildlife, Marine Region, Eureka, California, 95501, USA
| | - Avishek Chakraborty
- Department of Mathematical Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - J Wilson White
- Department of Fisheries and Wildlife, Coastal Oregon Marine Experiment Station, Oregon State University, Newport, Oregon, 97365, USA
| | - Marissa L Baskett
- Department of Environmental Science & Policy, University of California, Davis, California, 95616, USA
| | - Steven G Morgan
- Department of Environmental Science & Policy, University of California, Davis, California, 95616, USA
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14
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Movements and behaviour of blue whales satellite tagged in an Australian upwelling system. Sci Rep 2020; 10:21165. [PMID: 33273533 PMCID: PMC7713308 DOI: 10.1038/s41598-020-78143-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/10/2020] [Indexed: 11/15/2022] Open
Abstract
Knowledge about the movement ecology of endangered species is needed to identify biologically important areas and the spatio-temporal scale of potential human impacts on species. Blue whales (Balaenoptera musculus) are endangered due to twentieth century whaling and currently threatened by human activities. In Australia, they feed in the Great Southern Australian Coastal Upwelling System (GSACUS) during the austral summer. We investigate their movements, occupancy, behaviour, and environmental drivers to inform conservation management. Thirteen whales were satellite tagged, biopsy sampled and photo-identified in 2015. All were genetically confirmed to be of the pygmy subspecies (B. m. brevicauda). In the GSACUS, whales spent most of their time over the continental shelf and likely foraging in association with several seascape variables (sea surface temperature variability, depth, wind speed, sea surface height anomaly, and chlorophyll a). When whales left the region, they migrated west and then north along the Australian coast until they reached West Timor and Indonesia, where their movements indicated breeding or foraging behaviour. These results highlight the importance of the GSACUS as a foraging ground for pygmy blue whales inhabiting the eastern Indian Ocean and indicate the whales’ migratory route to proposed breeding grounds off Indonesia. Information about the spatio-temporal scale of potential human impacts can now be used to protect this little-known subspecies of blue whale.
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15
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Søltoft-Jensen A, Heide-Jørgensen MP, Ditlevsen S. Modelling the sound production of narwhals using a point process framework with memory effects. Ann Appl Stat 2020. [DOI: 10.1214/20-aoas1379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Jullum M. Investigating mesh‐based approximation methods for the normalization constant in the log Gaussian Cox process likelihood. Stat (Int Stat Inst) 2020. [DOI: 10.1002/sta4.285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Martin Jullum
- Department of Statistical Analysis, Image Analysis, and Pattern Recognition Norwegian Computing Center Oslo NO‐0314 Norway
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17
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Glennie R, Buckland ST, Langrock R, Gerrodette T, Ballance LT, Chivers SJ, Scott MD. Incorporating Animal Movement Into Distance Sampling. J Am Stat Assoc 2020. [DOI: 10.1080/01621459.2020.1764362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- R. Glennie
- School of Mathematics and Statistics, Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, UK
| | - S. T. Buckland
- School of Mathematics and Statistics, Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, UK
| | - R. Langrock
- Department of Business Administration and Economics, Bielefeld University, Bielefeld, Germany
| | - T. Gerrodette
- Southwest Fisheries Science Centre, NOAA Fisheries, La Jolla, CA
| | - L. T. Ballance
- Southwest Fisheries Science Centre, NOAA Fisheries, La Jolla, CA
| | - S. J. Chivers
- Southwest Fisheries Science Centre, NOAA Fisheries, La Jolla, CA
| | - M. D. Scott
- Inter-American Tropical Tuna Commission, California, La Jolla, CA
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18
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Becker EA, Carretta JV, Forney KA, Barlow J, Brodie S, Hoopes R, Jacox MG, Maxwell SM, Redfern JV, Sisson NB, Welch H, Hazen EL. Performance evaluation of cetacean species distribution models developed using generalized additive models and boosted regression trees. Ecol Evol 2020; 10:5759-5784. [PMID: 32607189 PMCID: PMC7319248 DOI: 10.1002/ece3.6316] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 11/25/2022] Open
Abstract
Species distribution models (SDMs) are important management tools for highly mobile marine species because they provide spatially and temporally explicit information on animal distribution. Two prevalent modeling frameworks used to develop SDMs for marine species are generalized additive models (GAMs) and boosted regression trees (BRTs), but comparative studies have rarely been conducted; most rely on presence-only data; and few have explored how features such as species distribution characteristics affect model performance. Since the majority of marine species BRTs have been used to predict habitat suitability, we first compared BRTs to GAMs that used presence/absence as the response variable. We then compared results from these habitat suitability models to GAMs that predict species density (animals per km2) because density models built with a subset of the data used here have previously received extensive validation. We compared both the explanatory power (i.e., model goodness of fit) and predictive power (i.e., performance on a novel dataset) of the GAMs and BRTs for a taxonomically diverse suite of cetacean species using a robust set of systematic survey data (1991-2014) within the California Current Ecosystem. Both BRTs and GAMs were successful at describing overall distribution patterns throughout the study area for the majority of species considered, but when predicting on novel data, the density GAMs exhibited substantially greater predictive power than both the presence/absence GAMs and BRTs, likely due to both the different response variables and fitting algorithms. Our results provide an improved understanding of some of the strengths and limitations of models developed using these two methods. These results can be used by modelers developing SDMs and resource managers tasked with the spatial management of marine species to determine the best modeling technique for their question of interest.
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Affiliation(s)
- Elizabeth A. Becker
- National Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationOcean Associates, Inc., Under Contract to Southwest Fisheries Science CenterLa JollaCAUSA
- Institute of Marine ScienceUniversity of California Santa CruzSanta CruzCAUSA
- ManTech International CorporationSolana BeachCAUSA
| | - James V. Carretta
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCAUSA
| | - Karin A. Forney
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationMoss LandingCAUSA
- Moss Landing Marine LaboratoriesSan Jose State UniversityMoss LandingCAUSA
| | - Jay Barlow
- Marine Mammal and Turtle DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationLa JollaCAUSA
| | - Stephanie Brodie
- Institute of Marine ScienceUniversity of California Santa CruzSanta CruzCAUSA
- Environmental Research DivisionSouthwest Fisheries Science CenterMontereyCAUSA
| | - Ryan Hoopes
- ManTech International CorporationSolana BeachCAUSA
| | - Michael G. Jacox
- Environmental Research DivisionSouthwest Fisheries Science CenterMontereyCAUSA
- Physical Sciences DivisionEarth System Research LaboratoryBoulderCOUSA
| | - Sara M. Maxwell
- School of Interdisciplinary Arts and SciencesUniversity of WashingtonBothellWAUSA
| | | | | | - Heather Welch
- Institute of Marine ScienceUniversity of California Santa CruzSanta CruzCAUSA
- Environmental Research DivisionSouthwest Fisheries Science CenterMontereyCAUSA
| | - Elliott L. Hazen
- Institute of Marine ScienceUniversity of California Santa CruzSanta CruzCAUSA
- Environmental Research DivisionSouthwest Fisheries Science CenterMontereyCAUSA
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19
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Jullum M, Thorarinsdottir T, Bachl FE. Estimating seal pup production in the Greenland Sea by using Bayesian hierarchical modelling. J R Stat Soc Ser C Appl Stat 2020. [DOI: 10.1111/rssc.12397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Miller DL, Glennie R, Seaton AE. Understanding the Stochastic Partial Differential Equation Approach to Smoothing. JOURNAL OF AGRICULTURAL, BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2020. [DOI: 10.1007/s13253-019-00377-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Abstract
Correlation and smoothness are terms used to describe a wide variety of random quantities. In time, space, and many other domains, they both imply the same idea: quantities that occur closer together are more similar than those further apart. Two popular statistical models that represent this idea are basis-penalty smoothers (Wood in Texts in statistical science, CRC Press, Boca Raton, 2017) and stochastic partial differential equations (SPDEs) (Lindgren et al. in J R Stat Soc Series B (Stat Methodol) 73(4):423–498, 2011). In this paper, we discuss how the SPDE can be interpreted as a smoothing penalty and can be fitted using the package , allowing practitioners with existing knowledge of smoothing penalties to better understand the implementation and theory behind the SPDE approach.
Supplementary materials accompanying this paper appear online.
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Konstantinoudis G, Schuhmacher D, Rue H, Spycher BD. Discrete versus continuous domain models for disease mapping. Spat Spatiotemporal Epidemiol 2020; 32:100319. [PMID: 32007284 DOI: 10.1016/j.sste.2019.100319] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/04/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
The main goal of disease mapping is to estimate disease risk and identify high-risk areas. Such analyses are hampered by the limited geographical resolution of the available data. Typically the available data are counts per spatial unit and the common approach is the Besag-York-Mollié (BYM) model. When precise geocodes are available, it is more natural to use Log-Gaussian Cox processes (LGCPs). In a simulation study mimicking childhood leukaemia incidence using actual residential locations of all children in the canton of Zürich, Switzerland, we compare the ability of these models to recover risk surfaces and identify high-risk areas. We then apply both approaches to actual data on childhood leukaemia incidence in the canton of Zürich during 1985-2015. We found that LGCPs outperform BYM models in almost all scenarios considered. Our findings suggest that there are important gains to be made from the use of LGCPs in spatial epidemiology.
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Affiliation(s)
| | | | - Håvard Rue
- CEMSE Division, King Abdullah University of Science and Technology, Saudi Arabia.
| | - Ben D Spycher
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland.
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22
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Joseph MB. Neural hierarchical models of ecological populations. Ecol Lett 2020; 23:734-747. [PMID: 31970895 DOI: 10.1111/ele.13462] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/17/2019] [Accepted: 12/23/2019] [Indexed: 01/20/2023]
Abstract
Neural networks are increasingly being used in science to infer hidden dynamics of natural systems from noisy observations, a task typically handled by hierarchical models in ecology. This article describes a class of hierarchical models parameterised by neural networks - neural hierarchical models. The derivation of such models analogises the relationship between regression and neural networks. A case study is developed for a neural dynamic occupancy model of North American bird populations, trained on millions of detection/non-detection time series for hundreds of species, providing insights into colonisation and extinction at a continental scale. Flexible models are increasingly needed that scale to large data and represent ecological processes. Neural hierarchical models satisfy this need, providing a bridge between deep learning and ecological modelling that combines the function representation power of neural networks with the inferential capacity of hierarchical models.
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Affiliation(s)
- Maxwell B Joseph
- Earth Lab, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80303, USA
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23
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Renner IW, Louvrier J, Gimenez O. Combining multiple data sources in species distribution models while accounting for spatial dependence and overfitting with combined penalized likelihood maximization. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ian W. Renner
- School of Mathematical and Physical Sciences The University of Newcastle Callaghan Australia
| | - Julie Louvrier
- Department of Ecological Dynamics Department of Evolutionary Ecology Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Olivier Gimenez
- CEFECNRSUniv MontpellierUniv Paul Valéry Montpellier 3EPHEIRD Montpellier France
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24
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Bowler DE, Nilsen EB, Bischof R, O'Hara RB, Yu TT, Oo T, Aung M, Linnell JDC. Integrating data from different survey types for population monitoring of an endangered species: the case of the Eld's deer. Sci Rep 2019; 9:7766. [PMID: 31123274 PMCID: PMC6533261 DOI: 10.1038/s41598-019-44075-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/08/2019] [Indexed: 11/30/2022] Open
Abstract
Despite its value for conservation decision-making, we lack information on population abundances for most species. Because establishing large-scale monitoring schemes is rarely feasible, statistical methods that combine multiple data sources are promising approaches to maximize use of available information. We built a Bayesian hierarchical model that combined different survey data of the endangered Eld’s deer in Shwesettaw Wildlife Sanctuary (SWS) in Myanmar and tested our approach in simulation experiments. We combined spatially-restricted line-transect abundance data with more spatially-extensive camera-trap occupancy data to enable estimation of the total deer abundance. The integrated model comprised an ecological model (common to both survey types, based on the equivalence between cloglog-transformed occurrence probability and log-transformed expected abundance) and separate observation models for each survey type. We estimated that the population size of Eld’s deer in SWS is c. 1519 (1061–2114), suggesting it is the world’s largest wild population. The simulations indicated that the potential benefits of combining data include increased precision and better sampling of the spatial variation in the environment, compared to separate analysis of each survey. Our analytical approach, which integrates the strengths of different survey methods, has widespread application for estimating species’ abundances, especially in information-poor regions of the world.
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Affiliation(s)
- Diana E Bowler
- Norwegian Institute for Nature Research - NINA, Box 5685 Torgard, NO-7485, Trondheim, Norway.
| | - Erlend B Nilsen
- Norwegian Institute for Nature Research - NINA, Box 5685 Torgard, NO-7485, Trondheim, Norway
| | - Richard Bischof
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Box 5003, NO-1432, Ås, Norway
| | - Robert B O'Hara
- Department of Mathematical Sciences, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Thin Thin Yu
- Nature and Wildlife Conservation Division, Ministry of Natural Resources and Environmental Conservation, Nay Pyi Taw, Myanmar
| | - Tun Oo
- Friends of Wildlife, Room 15, Building 296, Yang-Aung Street, Yankin Township, Yangon, Myanmar
| | - Myint Aung
- Friends of Wildlife, Room 15, Building 296, Yang-Aung Street, Yankin Township, Yangon, Myanmar
| | - John D C Linnell
- Norwegian Institute for Nature Research - NINA, Box 5685 Torgard, NO-7485, Trondheim, Norway
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Affiliation(s)
- Res Altwegg
- Statistics in Ecology, Environment and Conservation, Department of Statistical SciencesUniversity of Cape Town Rondebosch South Africa
- African Climate and Development InitiativeUniversity of Cape Town Rondebosch South Africa
| | - James D. Nichols
- Patuxent Wildlife Research CenterUS Geological Survey Laurel Maryland
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Becker EA, Forney KA, Redfern JV, Barlow J, Jacox MG, Roberts JJ, Palacios DM. Predicting cetacean abundance and distribution in a changing climate. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12867] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Elizabeth A. Becker
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
- ManTech International Corporation Solana Beach California
| | - Karin A. Forney
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration Moss Landing California
- Moss Landing Marine Laboratories Moss Landing California
| | - Jessica V. Redfern
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Jay Barlow
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration La Jolla California
| | - Michael G. Jacox
- Environmental Research Division Southwest Fisheries Science Center Monterey California
- Physical Sciences Division Earth System Research Laboratory Boulder Colorado
| | - Jason J. Roberts
- Marine Geospatial Ecology Laboratory, Nicholas School of the Environment Duke University Durham North Carolina
| | - Daniel M. Palacios
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center Oregon State University Newport Oregon
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27
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Bakka H, Rue H, Fuglstad G, Riebler A, Bolin D, Illian J, Krainski E, Simpson D, Lindgren F. Spatial modeling with R‐INLA: A review. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/wics.1443] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Haakon Bakka
- CEMSE Division King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Håvard Rue
- CEMSE Division King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Geir‐Arne Fuglstad
- Department of Mathematical Sciences Norwegian University of Science and Technology Trondheim Norway
| | - Andrea Riebler
- Department of Mathematical Sciences Norwegian University of Science and Technology Trondheim Norway
| | - David Bolin
- Department of Mathematical Sciences Chalmers University of Technology and University of Gothenburg Gothenburg Sweden
| | - Janine Illian
- CREEM, School of Mathematics and Statistics University of St Andrews St. Andrews UK
| | - Elias Krainski
- Departamento de Estatística Universidade Federal do Paraná Paraná Brazil
| | - Daniel Simpson
- Department of Statistical Sciences University of Toronto Toronto Canada
| | - Finn Lindgren
- School of Mathematics University of Edinburgh Edinburgh UK
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28
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Mäkinen J, Vanhatalo J. Hierarchical Bayesian model reveals the distributional shifts of Arctic marine mammals. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Jussi Mäkinen
- Organismal and Evolutionary Biology Research Program; Faculty of Biological and Environmental Sciences; University of Helsinki; Helsinki Finland
| | - Jarno Vanhatalo
- Organismal and Evolutionary Biology Research Program; Faculty of Biological and Environmental Sciences; University of Helsinki; Helsinki Finland
- Department of Mathematics and Statistics; Faculty of Science; University of Helsinki; Helsinki Finland
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29
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Yuan Y, Bachl FE, Lindgren F, Borchers DL, Illian JB, Buckland ST, Rue H, Gerrodette T. Point process models for spatio-temporal distance sampling data from a large-scale survey of blue whales. Ann Appl Stat 2017. [DOI: 10.1214/17-aoas1078] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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30
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Jones‐Todd CM, Swallow B, Illian JB, Toms M. A spatiotemporal multispecies model of a semicontinuous response. J R Stat Soc Ser C Appl Stat 2017. [DOI: 10.1111/rssc.12250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Ben Swallow
- University of St Andrews UK
- University of Warwick Coventry UK
| | | | - Mike Toms
- British Trust for Ornithology Thetford UK
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