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Integrated Population Models: Achieving Their Potential. JOURNAL OF STATISTICAL THEORY AND PRACTICE 2023. [DOI: 10.1007/s42519-022-00302-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
AbstractPrecise and accurate estimates of abundance and demographic rates are primary quantities of interest within wildlife conservation and management. Such quantities provide insight into population trends over time and the associated underlying ecological drivers of the systems. This information is fundamental in managing ecosystems, assessing species conservation status and developing and implementing effective conservation policy. Observational monitoring data are typically collected on wildlife populations using an array of different survey protocols, dependent on the primary questions of interest. For each of these survey designs, a range of advanced statistical techniques have been developed which are typically well understood. However, often multiple types of data may exist for the same population under study. Analyzing each data set separately implicitly discards the common information contained in the other data sets. An alternative approach that aims to optimize the shared information contained within multiple data sets is to use a “model-based data integration” approach, or more commonly referred to as an “integrated model.” This integrated modeling approach simultaneously analyzes all the available data within a single, and robust, statistical framework. This paper provides a statistical overview of ecological integrated models, with a focus on integrated population models (IPMs) which include abundance and demographic rates as quantities of interest. Four main challenges within this area are discussed, namely model specification, computational aspects, model assessment and forecasting. This should encourage researchers to explore further and develop new practical tools to ensure that full utility can be made of IPMs for future studies.
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Bird SM, King R. Multiple Systems Estimation (or Capture-Recapture Estimation) to Inform Public Policy. ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION 2018; 5:95-118. [PMID: 30046636 PMCID: PMC6055983 DOI: 10.1146/annurev-statistics-031017-100641] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Estimating population sizes has long been of interest, from the estimation of the human or ecological population size within regions or countries to the hidden number of civilian casualties in a war. Total enumeration of the population, for example, via a census, is often infeasible or simply impractical. However, a series of partial enumerations or observations of the population is often possible. This has led to the ideas of capture-recapture methods, which have been extensively used within ecology to estimate the size of wildlife populations, with an associated measure of uncertainty, and are most effectively applied when there are multiple capture occasions. Capture-recapture ideology can be more widely applied to multiple data-sources, by the linkage of individuals across the multiple lists. This is often referred to as Multiple Systems Estimation (MSE). The MSE approach has been preferred when estimating "capture-shy" or hard-to-reach populations, including those caught up in the criminal justice system; or homeless; or trafficked; or civilian casualties of war. Motivated by a range of public policy applications of MSE, each briefly introduced, we discuss practical problems with potentially substantial methodological implications. They include: "period" definition; "case" definition; when an observed count is not a true count of the population of interest but an upper bound due to mismatched definitions; exact or probabilistic matching of "cases" across different lists; demographic or other information about the "case" which may influence capture-propensities; required permissions to access extant-lists; list-creation by research-teams or interested parties; referrals (if presence on list A results - almost surely - in presence on list B); different mathematical models leading to widely different estimated population sizes; uncertainty in estimation; computational efficiency; external validation; hypothesis-generation; and additional independent external information. Returning to our motivational applications, we focus on whether the uncertainty which qualified their estimates was sufficiently narrow to orient public policy; and, if not, what options were available and/or taken to reduce the uncertainty or to seek external validation. We also consider whether MSE was hypothesis-generating: in the sense of having spawned new lines of inquiry.
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Affiliation(s)
- Sheila M Bird
- MRC Biostatistics Unit, University of Cambridge School of Clinical Medicine, Institute for Public Health Cambridge CB2 0SR
- University of Edinburgh, Usher Institute of Population Health Sciences and Informatics, Edinburgh EH16 4UX
| | - Ruth King
- University of Edinburgh, School of Mathematics, Edinburgh EH9 3FD
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Wanelik KM, Burthe SJ, Harris MP, Nunn MA, Godfray HCJ, Sheldon BC, McLean AR, Wanless S. Investigating the effects of age-related spatial structuring on the transmission of a tick-borne virus in a colonially breeding host. Ecol Evol 2017; 7:10930-10940. [PMID: 29299270 PMCID: PMC5743484 DOI: 10.1002/ece3.3612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/20/2017] [Accepted: 10/16/2017] [Indexed: 11/11/2022] Open
Abstract
Higher pathogen and parasite transmission is considered a universal cost of colonial breeding due to the physical proximity of colony members. However, this has rarely been tested in natural colonies, which are structured entities, whose members interact with a subset of individuals and differ in their infection histories. We use a population of common guillemots, Uria aalge, infected by a tick-borne virus, Great Island virus, to explore how age-related spatial structuring can influence the infection costs borne by different members of a breeding colony. Previous work has shown that the per-susceptible risk of infection (force of infection) is different for prebreeding (immature) and breeding (adult) guillemots which occupy different areas of the colony. We developed a mathematical model which showed that this difference in infection risk can only be maintained if mixing between these age groups is low. To estimate mixing between age groups, we recorded the movements of 63 individually recognizable, prebreeding guillemots in four different parts of a major colony in the North Sea during the breeding season. Prebreeding guillemots infrequently entered breeding areas (in only 26% of watches), though with marked differences in frequency of entry among individuals and more entries toward the end of the breeding season. Once entered, the proportion of time spent in breeding areas by prebreeding guillemots also varied between different parts of the colony. Our data and model predictions indicate low levels of age-group mixing, limiting exposure of breeding guillemots to infection. However, they also suggest that prebreeding guillemots have the potential to play an important role in driving infection dynamics. This highlights the sensitivity of breeding colonies to changes in the behavior of their members-a subject of particular importance in the context of global environmental change.
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Affiliation(s)
- Klara M Wanelik
- Department of Zoology University of Oxford Oxford UK.,Centre for Ecology & Hydrology Wallingford UK.,Institute of Integrative Biology University of Liverpool Liverpool UK
| | | | | | | | | | - Ben C Sheldon
- Department of Zoology University of Oxford Oxford UK
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Sadykova D, Scott BE, De Dominicis M, Wakelin SL, Sadykov A, Wolf J. Bayesian joint models with INLA exploring marine mobile predator-prey and competitor species habitat overlap. Ecol Evol 2017; 7:5212-5226. [PMID: 29242741 PMCID: PMC5528225 DOI: 10.1002/ece3.3081] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/05/2017] [Accepted: 05/08/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding spatial physical habitat selection driven by competition and/or predator–prey interactions of mobile marine species is a fundamental goal of spatial ecology. However, spatial counts or density data for highly mobile animals often (1) include excess zeros, (2) have spatial correlation, and (3) have highly nonlinear relationships with physical habitat variables, which results in the need for complex joint spatial models. In this paper, we test the use of Bayesian hierarchical hurdle and zero‐inflated joint models with integrated nested Laplace approximation (INLA), to fit complex joint models to spatial patterns of eight mobile marine species (grey seal, harbor seal, harbor porpoise, common guillemot, black‐legged kittiwake, northern gannet, herring, and sandeels). For each joint model, we specified nonlinear smoothed effect of physical habitat covariates and selected either competing species or predator–prey interactions. Out of a range of six ecologically important physical and biologic variables that are predicted to change with climate change and large‐scale energy extraction, we identified the most important habitat variables for each species and present the relationships between these bio/physical variables and species distributions. In particular, we found that net primary production played a significant role in determining habitat preferences of all the selected mobile marine species. We have shown that the INLA method is well‐suited for modeling spatially correlated data with excessive zeros and is an efficient approach to fit complex joint spatial models with nonlinear effects of covariates. Our approach has demonstrated its ability to define joint habitat selection for both competing and prey–predator species that can be relevant to numerous issues in the management and conservation of mobile marine species.
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Affiliation(s)
- Dinara Sadykova
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen UK.,School of Biological Sciences Queen's University Belfast Belfast UK
| | - Beth E Scott
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen UK
| | | | | | - Alexander Sadykov
- The Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
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Lahoz-Monfort JJ, Harris MP, Wanless S, Freeman SN, Morgan BJT. Bringing It All Together: Multi-species Integrated Population Modelling of a Breeding Community. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2017; 22:140-160. [PMID: 32103881 PMCID: PMC7010376 DOI: 10.1007/s13253-017-0279-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 04/03/2017] [Indexed: 10/29/2022]
Abstract
Integrated population models (IPMs) combine data on different aspects of demography with time-series of population abundance. IPMs are becoming increasingly popular in the study of wildlife populations, but their application has largely been restricted to the analysis of single species. However, species exist within communities: sympatric species are exposed to the same abiotic environment, which may generate synchrony in the fluctuations of their demographic parameters over time. Given that in many environments conditions are changing rapidly, assessing whether species show similar demographic and population responses is fundamental to quantifying interspecific differences in environmental sensitivity and highlighting ecological interactions at risk of disruption. In this paper, we combine statistical approaches to study populations, integrating data along two different dimensions: across species (using a recently proposed framework to quantify multi-species synchrony in demography) and within each species (using IPMs with demographic and abundance data). We analyse data from three seabird species breeding at a nationally important long-term monitoring site. We combine demographic datasets with island-wide population counts to construct the first multi-species Integrated Population Model to consider synchrony. Our extension of the IPM concept allows the simultaneous estimation of demographic parameters, adult abundance and multi-species synchrony in survival and productivity, within a robust statistical framework. The approach is readily applicable to other taxa and habitats. Supplementary materials accompanying this paper appear on-line. Electronic Supplementary Material Supplementary materials for this article are available at 10.1007/s13253-017-0279-4.
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Affiliation(s)
- José J Lahoz-Monfort
- 1School of BioSciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Michael P Harris
- 2Centre for Ecology and Hydrology, Bush Estate, Penicuik, Midlothian EH26 0QB UK
| | - Sarah Wanless
- 2Centre for Ecology and Hydrology, Bush Estate, Penicuik, Midlothian EH26 0QB UK
| | - Stephen N Freeman
- 3Centre for Ecology and Hydrology, Maclean Building, Crowmarsh Gifford, Wallingford, Oxfordshire OX10 8BB UK
| | - Byron J T Morgan
- 4National Centre for Statistical Ecology, School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, Kent CT2 7FS UK
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Cole DJ, McCrea RS. Parameter redundancy in discrete state-space and integrated models. Biom J 2016; 58:1071-90. [PMID: 27362826 PMCID: PMC5031231 DOI: 10.1002/bimj.201400239] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/05/2016] [Accepted: 04/21/2016] [Indexed: 01/20/2023]
Abstract
Discrete state-space models are used in ecology to describe the dynamics of wild animal populations, with parameters, such as the probability of survival, being of ecological interest. For a particular parametrization of a model it is not always clear which parameters can be estimated. This inability to estimate all parameters is known as parameter redundancy or a model is described as nonidentifiable. In this paper we develop methods that can be used to detect parameter redundancy in discrete state-space models. An exhaustive summary is a combination of parameters that fully specify a model. To use general methods for detecting parameter redundancy a suitable exhaustive summary is required. This paper proposes two methods for the derivation of an exhaustive summary for discrete state-space models using discrete analogues of methods for continuous state-space models. We also demonstrate that combining multiple data sets, through the use of an integrated population model, may result in a model in which all parameters are estimable, even though models fitted to the separate data sets may be parameter redundant.
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Affiliation(s)
- Diana J Cole
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, Kent CT2 7NF, England.
| | - Rachel S McCrea
- School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, Kent CT2 7NF, England
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Predicting Future European Breeding Distributions of British Seabird Species under Climate Change and Unlimited/No Dispersal Scenarios. DIVERSITY-BASEL 2015. [DOI: 10.3390/d7040342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Reed TE, Harris MP, Wanless S. Skipped breeding in common guillemots in a changing climate: restraint or constraint? Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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King R, McCrea R. A generalised likelihood framework for partially observed capture–recapture–recovery models. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.stamet.2013.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lahoz-Monfort JJ, Harris MP, Morgan BJT, Freeman SN, Wanless S. Exploring the consequences of reducing survey effort for detecting individual and temporal variability in survival. J Appl Ecol 2014. [DOI: 10.1111/1365-2664.12214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José J. Lahoz-Monfort
- National Centre for Statistical Ecology; School of Mathematics, Statistics & Actuarial Science; University of Kent; Canterbury Kent CT2 7NF UK
- Centre for Ecology & Hydrology; Maclean Building Crowmarsh Gifford Wallingford Oxfordshire OX10 8BB UK
- School of Botany; University of Melbourne; Parkville Vic. 3010 Australia
| | - Michael P. Harris
- Centre for Ecology & Hydrology; Bush Estate; Penicuik Midlothian EH26 0QB UK
| | - Byron J. T. Morgan
- National Centre for Statistical Ecology; School of Mathematics, Statistics & Actuarial Science; University of Kent; Canterbury Kent CT2 7NF UK
| | - Stephen N. Freeman
- Centre for Ecology & Hydrology; Maclean Building Crowmarsh Gifford Wallingford Oxfordshire OX10 8BB UK
| | - Sarah Wanless
- Centre for Ecology & Hydrology; Bush Estate; Penicuik Midlothian EH26 0QB UK
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Frederiksen M, Lebreton JD, Pradel R, Choquet R, Gimenez O. REVIEW: Identifying links between vital rates and environment: a toolbox for the applied ecologist. J Appl Ecol 2013. [DOI: 10.1111/1365-2664.12172] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Morten Frederiksen
- Department of Bioscience; Aarhus University; Frederiksborgvej 399 DK-4000 Roskilde Denmark
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175; Campus CNRS 1919 route de Mende F-34293 Montpellier Cedex 5 France
| | - Jean-Dominique Lebreton
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175; Campus CNRS 1919 route de Mende F-34293 Montpellier Cedex 5 France
| | - Roger Pradel
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175; Campus CNRS 1919 route de Mende F-34293 Montpellier Cedex 5 France
| | - Rémi Choquet
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175; Campus CNRS 1919 route de Mende F-34293 Montpellier Cedex 5 France
| | - Olivier Gimenez
- Centre d'Ecologie Fonctionnelle et Evolutive; UMR 5175; Campus CNRS 1919 route de Mende F-34293 Montpellier Cedex 5 France
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Illian JB, Martino S, Sørbye SH, Gallego-Fernández JB, Zunzunegui M, Esquivias MP, Travis JMJ. Fitting complex ecological point process models with integrated nested Laplace approximation. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12017] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janine B. Illian
- CREEM; School of Mathematics and Statistics; University of St Andrews; St Andrews; Fife; KY16 9LZ; UK
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A Bayesian Approach to Fitting Gibbs Processes with Temporal Random Effects. JOURNAL OF AGRICULTURAL, BIOLOGICAL, AND ENVIRONMENTAL STATISTICS 2012. [DOI: 10.1007/s13253-012-0111-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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McCrea RS, Morgan BJT, Cole DJ. Age-dependent mixture models for recovery data on animals marked at unknown age. J R Stat Soc Ser C Appl Stat 2012. [DOI: 10.1111/j.1467-9876.2012.01043.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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OOSTHUIZEN WCHRIS, DE BRUYN PJNICO, BESTER MARTHÁNN. Unmarked individuals in mark-recapture studies: Comparisons of marked and unmarked southern elephant seals at Marion Island. AUSTRAL ECOL 2011. [DOI: 10.1111/j.1442-9993.2011.02316.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Smout S, King R, Pomeroy P. Integrating heterogeneity of detection and mark loss to estimate survival and transience in UK grey seal colonies. J Appl Ecol 2010. [DOI: 10.1111/j.1365-2664.2010.01913.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Multi-Site Integrated Population Modelling. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2010. [DOI: 10.1007/s13253-010-0027-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Juillet C, Choquet R, Gauthier G, Pradel R. A Capture–Recapture Model with Double-Marking, Live and Dead Encounters, and Heterogeneity of Reporting Due to Auxiliary Mark Loss. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2010. [DOI: 10.1007/s13253-010-0035-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abadi F, Gimenez O, Ullrich B, Arlettaz R, Schaub M. Estimation of immigration rate using integrated population models. J Appl Ecol 2010. [DOI: 10.1111/j.1365-2664.2010.01789.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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An Integrated Population Model From Constant Effort Bird-Ringing Data. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2010. [DOI: 10.1007/s13253-009-0001-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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