Modelling spatial distribution and change from wildlife survey data
Lead Research Organisation:
University of Edinburgh
Department Name: Sch of Mathematics
Abstract
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Organisations
People |
ORCID iD |
| Finn Lindgren (Principal Investigator) |
Publications
Bachl F
(2019)
inlabru: an R package for Bayesian spatial modelling from ecological survey data
in Methods in Ecology and Evolution
Bayliss K
(2020)
Data-Driven Optimization of Seismicity Models Using Diverse Data Sets: Generation, Evaluation, and Ranking Using Inlabru
in Journal of Geophysical Research: Solid Earth
Bell O
(2021)
Isotopic niche variation in Tasmanian devils Sarcophilus harrisii with progression of devil facial tumor disease.
in Ecology and evolution
Cunningham CA
(2021)
Translating area-based conservation pledges into efficient biodiversity protection outcomes.
in Communications biology
Jiao J
(2021)
Heterogeneity pursuit for spatial point pattern with application to tree locations: A Bayesian semiparametric recourse
in Environmetrics
Martino S
(2021)
Integration of presence-only data from several sources: a case study on dolphins' spatial distribution
in Ecography
Nightingale G
(2021)
How does the community COVID-19 level of risk impact on that of a care home?
in PloS one
Williamson L
(2021)
Spatiotemporal variation in harbor porpoise distribution and foraging across a landscape of fear
in Marine Mammal Science
Yuan Y
(2017)
Point process models for spatio-temporal distance sampling data from a large-scale survey of blue whales
in The Annals of Applied Statistics
Yuan, Y
(2017)
Point process models for spatio-temporal distance sampling data from a large-scale survey of blue whales
in Annals of Applied Statistics
| Description | We have developed inference methods for spatial modelling (predicting abundance and distribution of wildlife, and how this changes over time) from survey data gathered using distance sampling methods (in which a key datum is distance of detected individuals from the surveyor). A software package (inlabru, in the statistical programming language R) has been developed to implement these methods, and placed on the international R package repository: https://cran.r-project.org/package=inlabru |
| Exploitation Route | Our methods are being investigated by researchers in the USA National Oceanic and Atmospheric Administration to model the spatial and spatio-temporal distribution of dolphins and whales in the Eastern Tropical Pacific. To date this has uncovered spatio-temporal patterns for one species that previous analyses failed to pick up. Our methods are also being applied to survey data from pre- and post-construction phases of offshore wind farms, to assess their efficacy in detecting impact of wind farm construction on local species. Scientists from the British Trust for Ornithology, the Joint Nature Conservancy, and other conservation organizations have expressed interest in the methods. |
| Sectors | Energy,Environment |
| URL | http://inlabru.org |
| Description | The inlabru software is becoming increasingly used for general spatial and spatio-temporal modelling applications. Since its initial release in 2017, the package has been downloaded almost 30000 times from one of the common R package servers hosted by RStudio. Applications that have used inlabru include species abundance estimation in ecology, seismicity modelling for earthquake forecasting, as well as spatial sports analysis. Up to 2020, we ran 6 professional training workshops for academics and professionals interested in using the methods; the largest, week-long workshop in 2018 had over 27 registered participants. Due to the pandemic no workshops were held in 2020 or 2021, but a new training workshop is planned to take place in 2022. |
| First Year Of Impact | 2017 |
| Sector | Environment,Healthcare,Leisure Activities, including Sports, Recreation and Tourism |
| Title | Spatial modelling of point data with unknown detection or thinning probabilities |
| Description | This new data analysis technique allows simultaneous estimation of spatial point process models and detection probabilities, from point data that are obtained in such a way that some points are missed and the probability of missing or detecting points is unknown. Such data are very common in ecological surveys. |
| Type Of Material | Data analysis technique |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | None as yet - model is very new. |
| URL | https://sites.google.com/inlabru.org/inlabru |
| Title | inlabru: Bayesian Latent Gaussian Modelling using INLA and Extensions |
| Description | An R package to do spatial and spatio-temporal point process modelling from census, plot sampling and distance sampling data. The package integrates survey models for census, plot sampling and distance sampling methods with spatial and spatio-temporal point process modelling methods to allow fully model-based inference from ecological survey and other point sample data. It uses the R-INLA package to implement Bayesian inference methods. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | We have given two workshops in St Andrews to train users to use the software, attracting XX people from YY countries. We have also given two invited training workshops that attracted a total of 71 participants. Participants at workshops included postgraduate students, conservation professionals and wildlife managers from governmental, international and private organisations, academic statisticians and ecologists. We have been invited to give a workshop on our software and methods at the premier international conference from ecological statisticians (The International Statistical Ecology Conference: http://www.isec2018.org/27754) in 2018. We have established collaborations with Marine Scotland Science, the Wildlife Conservation Society, the Tanzania Conservation Resource Centre and the South African National Biodiversity Institute, to use the software to address problems faced by these organisations. A manuscript describing and illustrating the software capabilities has been submitted to Methods in Ecology and Evolution. |
| URL | http://inlabru.org/ |
| Description | AMLGM2016 presentation (Trondheim, Norway) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Finn Lindgren and Fabian Bachl presented details on the methods and software from the project, leading to valuable feedback on the software interface and increased interest in the methods. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://amlgm2016.r-inla.org/ |
| Description | Invited talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk at International Conference on Advances in Interdisciplinary Statistics and Combinatorics, 8th-10th October 2021 University of North Carolina at Greensboro |
| Year(s) Of Engagement Activity | 2021 |
| Description | LGM2016 conference presentation (Bath) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Fabian Bachl presented the methods developed in the project to the 54 participants of the conference, generating interest in the software package. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://lgm2016.r-inla.org/ |
| Description | Manchester seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | 15 postgraduate students and academic staff attended a research seminar that presented the software interface of inlabru, and the underlying mathematical theory, raising interest in using the package, as well as informing those who were already using it of new features. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Seminar talk on "Flexible modelling with inlabru: a distance sampling case study" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar at the University of Strathclyde, which prompted discussion of methods and software. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Software training workshop (St Andrews) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | 15 participants, including professionals from conservation organisations, academics in biology/ecology and postgraduate students, attended a 2-day training workshop in use of the iDistance software developed on this project, for modelling spatial and spatio-temporal distribution from distance sampling data. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Spatial Point Process Modelling with inlabru |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a 1-day training workshop, primarily for members of the National Centre for Statistical Ecology, to train them in use of the software (inlabru) and methods developed on the grant. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.kent.ac.uk/smsas/statistics/research/seak-news.html?view=380 |
| Description | TIES conference 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A presentation of the inlabru software package, and the new user interface and modelling features that have been added, to show practitioners the package capabilities. The presentation was in a session with several related presentations on applied spatial modelling, and the discussions have led to a research proposal being written to use inlabru to address new types of health data analysis. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://sites.google.com/view/tiesgraspa2021/invited-sessions |
| Description | Talk at The National Centre for Statistical Ecology meeting, Edinburgh, UK, on "Demystifying the SPDE approach to spatial modelling" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | 50-60 academics, students and practitioners attended this talk at a national conference. Various participants expressed interest in the methods and approach. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Workshop on Spatial Point Process Models for Ecological Survey Data with INLA. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a 4-day professional training workshop held at the University of St Andrews, to train participants in the methods developed on the grant, and in use of the software developed on the grant. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.creem.st-andrews.ac.uk/workshop-on-spatial-point-process-models-for-ecological-survey-da... |
| Description | inlabru training workshop (Cape Town, South Africa) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 35 participants, including academics in biology/ecology and postgraduate students, attended a 3 day training workshop in the use of the inlabru software developed in this project, for modelling spatial and spatio-temporal distributions from distance sampling data. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://synergy.st-andrews.ac.uk/essmod/2016/11/30/workshop-on-point-process-modelling-with-inla-cap... |
| Description | invited talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | invited talk at meeting by British/Irish Region of the International Biometric Society on "Topics in advanced sampling for efficient estimation and monitoring" |
| Year(s) Of Engagement Activity | 2021 |