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Damgaard C, Strandberg B, Ehlers B, Hansen RR, Strandberg MT. Effect of nitrogen and glyphosate on the plant community composition in a simulated field margin ecosystem: Model-based ordination of pin-point cover data. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120377. [PMID: 36228853 DOI: 10.1016/j.envpol.2022.120377] [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: 01/17/2022] [Revised: 08/15/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
The effect of nitrogen and glyphosate on the plant community composition was investigated in a simulated field margin ecosystem. The plant community composition was inferred from pin-point cover data using a model-based ordination method that is suited for modelling pin-point cover data. The mean structure of the ordination model is analogous to a standard linear model, which enabled us to estimate the mean effects of nitrogen and glyphosate and their interaction in the two-dimensional ordination space. There were significant effects of both nitrogen and glyphosate on the plant community composition and overall species diversity. The effects of nitrogen and glyphosate on the plant community composition differed significantly. Furthermore, the estimated combined effects of nitrogen and glyphosate indicated that nitrogen and glyphosate enforced the effect of each other on the plant community composition by synergistic interactions. Addition of nitrogen and glyphosate was found to favor a plant community that was dominated by perennial grasses, and there was a tendency for glyphosate to select for plant communities in which annual plants were more frequent. The results suggest that using the notion of plant functional types and specific knowledge of the degree of glyphosate tolerance may be effective for predicting the effect of glyphosate on the community composition.
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Affiliation(s)
- Christian Damgaard
- Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600, Silkeborg, Denmark.
| | - Beate Strandberg
- Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600, Silkeborg, Denmark
| | - Bodil Ehlers
- Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600, Silkeborg, Denmark
| | - Rikke Reisner Hansen
- Department of Ecoscience, Aarhus University, Vejlsøvej 25, 8600, Silkeborg, Denmark
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2
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Brindefalk B, Brolin H, Säve‐Söderbergh M, Karlsson E, Sundell D, Wikström P, Jacobsson K, Toljander J, Stenberg P, Sjödin A, Dryselius R, Forsman M, Ahlinder J. Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities. Microbiologyopen 2022; 11:e1320. [PMCID: PMC9511821 DOI: 10.1002/mbo3.1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Björn Brindefalk
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Melle Säve‐Söderbergh
- Science Division Swedish Food Agency Uppsala Sweden
- Institute of Environmental Medicine, Karolinska Institutet Stockholm Sweden
| | - Edvin Karlsson
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - David Sundell
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Per Wikström
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Karin Jacobsson
- Department of Biomedical Science and Veterinary Public Health Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Per Stenberg
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - Andreas Sjödin
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | | | - Mats Forsman
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Jon Ahlinder
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
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3
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Taranu ZE, Pinel‐Alloul B, Legendre P. Large‐scale multi‐trophic co‐response models and environmental control of pelagic food webs in Québec lakes. OIKOS 2020. [DOI: 10.1111/oik.07685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zofia E. Taranu
- Environnement et Changement Climatique Canada Montréal QC Canada
| | - Bernadette Pinel‐Alloul
- GRIL, Groupe de Recherche Interuniversitaire en Limnologie, Dépt de Sciences Biologiques, Univ. de Montréal, Montréal Montréal QC Canada
| | - Pierre Legendre
- GRIL, Groupe de Recherche Interuniversitaire en Limnologie, Dépt de Sciences Biologiques, Univ. de Montréal, Montréal Montréal QC Canada
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4
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Hui FKC, Hill NA, Welsh AH. Assuming independence in spatial latent variable models: Consequences and implications of misspecification. Biometrics 2020; 78:85-99. [PMID: 33340108 DOI: 10.1111/biom.13416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 11/30/2022]
Abstract
Multivariate spatial data, where multiple responses are simultaneously recorded across spatially indexed observational units, are routinely collected in a wide variety of disciplines. For example, the Southern Ocean Continuous Plankton Recorder survey collects records of zooplankton communities in the Indian sector of the Southern Ocean, with the aim of identifying and quantifying spatial patterns in biodiversity in response to environmental change. One increasingly popular method for modeling such data is spatial generalized linear latent variable models (GLLVMs), where the correlation across sites is captured by a spatial covariance function in the latent variables. However, little is known about the impact of misspecifying the latent variable correlation structure on inference of various parameters in such models. To address this gap in the literature, we investigate how misspecifying and assuming independence for the latent variables' correlation structure impacts estimation and inference in spatial GLLVMs. Through both theory and numerical studies, we show that performance of maximum likelihood estimation and inference on regression coefficients under misspecification depends on a combination of the response type, the magnitude of true regression coefficient, and the corresponding loadings, and, most importantly, whether the corresponding covariate is (also) spatially correlated. On the other hand, estimation and inference of truly nonzero loadings and prediction of latent variables is consistently not robust to misspecification of the latent variable correlation structure.
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Affiliation(s)
- Francis K C Hui
- Research School of Finance, Actuarial Studies & Statistics, Australian National University, Acton, Australia
| | - Nicole A Hill
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - A H Welsh
- Research School of Finance, Actuarial Studies & Statistics, Australian National University, Acton, Australia
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5
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Burner RC, Birkemoe T, Olsen SL, Sverdrup‐Thygeson A. Sampling beetle communities: Trap design interacts with weather and species traits to bias capture rates. Ecol Evol 2020; 10:14300-14308. [PMID: 33391716 PMCID: PMC7771183 DOI: 10.1002/ece3.7029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/29/2020] [Accepted: 10/28/2020] [Indexed: 11/10/2022] Open
Abstract
Globally, many insect populations are declining, prompting calls for action. Yet these findings have also prompted discussion about sampling methods and interpretation of long-term datasets. As insect monitoring and research efforts increase, it is critical to quantify the effectiveness of sampling methods. This is especially true if sampling biases of different methods covary with climate, which is also changing over time. We assess the effectiveness of two types of flight intercept traps commonly used for beetles, a diverse insect group responsible for numerous ecosystem services, under different climatic conditions in Norwegian boreal forest. One of these trap designs includes a device to prevent rainwater from entering the collection vial, diluting preservatives and flushing out beetles. This design is compared to a standard trap. We ask how beetle capture rates vary between these traps, and how these differences vary based on precipitation levels and beetle body size, an important species trait. Bayesian mixed models reveal that the standard and modified traps differ in their beetle capture rates, but that the magnitude and direction of these differences change with precipitation levels and beetle body size. At low rainfall levels, standard traps catch more beetles, but as precipitation increases the catch rates of modified traps overtake those of standard traps. This effect is most pronounced for large-bodied beetles. Sampling methods are known to differ in their effectiveness. Here, we present evidence for a less well-known but likely common phenomenon-an interaction between climate and sampling, such that relative effectiveness of trap types for beetle sampling differs depending on precipitation levels and species traits. This highlights a challenge for long-term monitoring programs, where both climate and insect populations are changing. Sampling methods should be sought that eliminate climate interactions, any biases should be quantified, and all insect datasets should include detailed methodological metadata.
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Affiliation(s)
- Ryan C. Burner
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | - Tone Birkemoe
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | | | - Anne Sverdrup‐Thygeson
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
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6
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Damgaard C, Hansen RR, Hui FK. Model-based ordination of pin-point cover data: Effect of management on dry heathland. ECOL INFORM 2020. [DOI: 10.1016/j.ecoinf.2020.101155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Tobler MW, Kéry M, Hui FKC, Guillera‐Arroita G, Knaus P, Sattler T. Joint species distribution models with species correlations and imperfect detection. Ecology 2019; 100:e02754. [DOI: 10.1002/ecy.2754] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/29/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Mathias W. Tobler
- San Diego Zoo Global Institute for Conservation Research 15600 San Pasqual Valley Road Escondido California 92027 USA
| | - Marc Kéry
- Swiss Ornithological Institute Seerose 1 6204 Sempach Switzerland
| | - Francis K. C. Hui
- Research School of Finance, Actuarial Studies & Statistics Australian National University Acton Australian Capital Territory 2601 Australia
| | | | - Peter Knaus
- Swiss Ornithological Institute Seerose 1 6204 Sempach Switzerland
| | - Thomas Sattler
- Swiss Ornithological Institute Seerose 1 6204 Sempach Switzerland
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8
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Yamaura Y, Blanchet FG, Higa M. Analyzing community structure subject to incomplete sampling: hierarchical community model vs. canonical ordinations. Ecology 2019; 100:e02759. [PMID: 31131887 DOI: 10.1002/ecy.2759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/17/2019] [Indexed: 11/11/2022]
Abstract
Recently developing hierarchical community models (HCMs) accounting for incomplete sampling are promising approaches to understand community organization. However, pros and cons of incorporating incomplete sampling in the analysis and related design issues remain unknown. In this study, we compared HCM and canonical redundancy analysis (RDA) carried out with 10 different dissimilarity coefficients to evaluate how each approach restores true community abundance data sampled with imperfect detection. We conducted simulation experiments with varying numbers of sampling sites, visits, mean detectability and mean abundance. Performance of HCM was measured by estimates of "expected" (mean) abundance ( λ ^ ij ) and realized abundance ( N ^ ij : direct estimate of site- and species-specific abundance). We also compared HCM and different types of RDA (normal, partial, and weighted), all performed with the same ten different dissimilarity coefficients, with unequal number of visits to sampling sites. In addition, we applied the models to a virtual survey carried out on the Barro Colorado Island tree plot data for which we know true community abundance. Simulation experiments showed that N ^ ij yielded by HCM best restored the underlying abundance of constituent species among 12 abundance estimates by HCM and RDA regardless if the sampling was equal or unequal. Mean abundance predominantly affected the performance of HCM and RDA while λ ^ ij yielded by HCM had comparable performance to percentage difference and Gower dissimilarity coefficients of RDA. Relative performance of RDA types depended on the combination of dissimilarity coefficients and the distribution of sampling effort. Best performance of N ^ ij followed by λ ^ ij , percentage difference and Gower dissimilarity were also observed for the analysis of tree plot data, and graphical plots (triplots) based on λ ^ ij rather than N ^ ij clearly separated the effects of two environmental covariates on the abundance of constituent species. Under our conditions of model evaluation and the method, we concluded that, in terms of assessing the environmental dependence of abundance, HCMs and RDA can have comparable performance if we can choose appropriate dissimilarity coefficients for RDA. However, since HCMs provide straightforward biological interpretations of parameter estimates and flexibility of the analysis, HCMs would be useful in many situations as well as conventional canonical ordinations.
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Affiliation(s)
- Yuichi Yamaura
- Department of Forest Vegetation, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, 305-8687, Japan.,Fenner School of Environment and Society, Australian National University, Canberra, Australian Capital Territory, 2601, Australia.,Shikoku Research Center, Forestry and Forest Products Research Institute, 2-915 Asakuranishi, Kochi, 780-8077, Japan
| | - F Guillaume Blanchet
- Department of Mathematics and Statistics, McMaster University, Hamilton Hall, Room 218, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Motoki Higa
- Faculty of Science and Technology, Kochi University, 2-5-1 Akebono-cho, Kochi, 780-8520, Japan
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9
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Wilkinson DP, Golding N, Guillera‐Arroita G, Tingley R, McCarthy MA. A comparison of joint species distribution models for presence–absence data. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13106] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David P. Wilkinson
- School of BioSciences University of Melbourne Parkville Victoria Australia
| | - Nick Golding
- School of BioSciences University of Melbourne Parkville Victoria Australia
| | | | - Reid Tingley
- School of BioSciences University of Melbourne Parkville Victoria Australia
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10
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Hui FKC, Tanaka E, Warton DI. Order selection and sparsity in latent variable models via the ordered factor LASSO. Biometrics 2018; 74:1311-1319. [PMID: 29750847 DOI: 10.1111/biom.12888] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/01/2018] [Accepted: 03/01/2018] [Indexed: 11/30/2022]
Abstract
Generalized linear latent variable models (GLLVMs) offer a general framework for flexibly analyzing data involving multiple responses. When fitting such models, two of the major challenges are selecting the order, that is, the number of factors, and an appropriate structure for the loading matrix, typically a sparse structure. Motivated by the application of GLLVMs to study marine species assemblages in the Southern Ocean, we propose the Ordered Factor LASSO or OFAL penalty for order selection and achieving sparsity in GLLVMs. The OFAL penalty is the first penalty developed specifically for order selection in latent variable models, and achieves this by using a hierarchically structured group LASSO type penalty to shrink entire columns of the loading matrix to zero, while ensuring that non-zero loadings are concentrated on the lower-order factors. Simultaneously, individual element sparsity is achieved through the use of an adaptive LASSO. In conjunction with using an information criterion which promotes aggressive shrinkage, simulation shows that the OFAL penalty performs strongly compared with standard methods and penalties for order selection, achieving sparsity, and prediction in GLLVMs. Applying the OFAL penalty to the Southern Ocean marine species dataset suggests the available environmental predictors explain roughly half of the total covariation between species, thus leading to a smaller number of latent variables and increased sparsity in the loading matrix compared to a model without any covariates.
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Affiliation(s)
- Francis K C Hui
- Mathematical Sciences Institute, The Australian National University, Acton, ACT 2601, Australia
| | - Emi Tanaka
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia
| | - David I Warton
- School of Mathematics and Statistics, and the Evolution & Ecology Research Centre, UNSW Sydney, NSW 2052, Australia
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11
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Martin RW, Waits ER, Nietch CT. Empirically-based modeling and mapping to consider the co-occurrence of ecological receptors and stressors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 613-614:1228-1239. [PMID: 28958130 PMCID: PMC6092948 DOI: 10.1016/j.scitotenv.2017.08.301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 05/22/2023]
Abstract
Part of the ecological risk assessment process involves examining the potential for environmental stressors and ecological receptors to co-occur across a landscape. In this study, we introduce a Bayesian joint modeling framework for use in evaluating and mapping the co-occurrence of stressors and receptors using empirical data, open-source statistical software, and Geographic Information Systems tools and data. To illustrate the approach, we apply the framework to bioassessment data on stream fishes and nutrients collected from a watershed in southwestern Ohio. The results highlighted the joint model's ability to parse and exploit statistical dependencies in order to provide empirical insight into the potential environmental and ecotoxicological interactions influencing co-occurrence. We also demonstrate how probabilistic predictions can be generated and mapped to visualize spatial patterns in co-occurrences. For practitioners, we believe that this data-driven approach to modeling and mapping co-occurrence can lead to more quantitatively transparent and robust assessments of ecological risk.
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Affiliation(s)
- Roy W Martin
- USEPA Office of Research and Development, Cincinnati, OH 45213, United States.
| | - Eric R Waits
- USEPA Office of Research and Development, Cincinnati, OH 45213, United States
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12
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Niku J, Warton DI, Hui FKC, Taskinen S. Generalized Linear Latent Variable Models for Multivariate Count and Biomass Data in Ecology. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2017. [DOI: 10.1007/s13253-017-0304-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Ovaskainen O, Tikhonov G, Norberg A, Guillaume Blanchet F, Duan L, Dunson D, Roslin T, Abrego N. How to make more out of community data? A conceptual framework and its implementation as models and software. Ecol Lett 2017; 20:561-576. [PMID: 28317296 DOI: 10.1111/ele.12757] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/31/2017] [Accepted: 02/09/2017] [Indexed: 12/23/2022]
Abstract
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities. We model environmental filtering by variation and covariation in the responses of individual species to the characteristics of their environment, with potential contingencies on species traits and phylogenetic relationships. We capture biotic assembly rules by species-to-species association matrices, which may be estimated at multiple spatial or temporal scales. We operationalise the HMSC framework as a hierarchical Bayesian joint species distribution model, and implement it as R- and Matlab-packages which enable computationally efficient analyses of large data sets. Armed with this tool, community ecologists can make sense of many types of data, including spatially explicit data and time-series data. We illustrate the use of this framework through a series of diverse ecological examples.
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Affiliation(s)
- Otso Ovaskainen
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Gleb Tikhonov
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Anna Norberg
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - F Guillaume Blanchet
- Department of Mathematics and Statistics, McMaster University, 1280 Main Street West Hamilton, Ontario, L8S 4K1, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boulevard Université Sherbrooke, Québec, J1K 2R1, Canada
| | - Leo Duan
- Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA
| | - David Dunson
- Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, 75651, Sweden
| | - Nerea Abrego
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.,Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, Helsinki, FI-00014, Finland
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