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ONLINE COURSE – Advanced Ecological Niche Modelling Using R (ANMR01) This course will be delivered online
25 January 2021 - 29 January 2021£560.00
Ecological niche, species distribution, habitat distribution, or climatic envelope models are different names for mechanistic and correlative models, which are empirical or mathematical approaches to the ecological niche of a species. These methods relate
different types of ecogeographical variables (environmental, topographical, human) to species physiological data or geographical locations, in order to identify the factors limiting and defining the species’ niche. ENMs have become popular because of their efficiency in the design and implementation of conservation management.
Have you built an Ecological Niche Model? If yes, you have already encountered challenges on data preparation, or have struggled with issues in models fitting and accuracy. This course will teach you how to overcome these challenges and improve the accuracy of your ecological niche models.
By the end of 5-day practical course you will have the capacity to
- filter records and select your variables with variance inflation factor;
- test the effect of Maxent regularization parameter in models performance;
- validate models performance and accuracy;
- perform MESS analysis, null models, and mechanistic models, as well as to build your “virtual species”.
Students will learn to use functions implemented in the packages “usdm”; “dismo”; “ENMEval”; “SDMvspecies”; “spThin”; and “NicheMapper” among others.
This is a ‘LIVE COURSE’ – the instructor will be delivering lectures and coaching attendees through the accompanying computer practical’s via video link, a good internet connection is essential.
TIME ZONE – Western European Time +1 – however all sessions will be recorded and made available allowing attendees from different time zones to follow a day behind with an additional 1/2 days support after the official course finish date (please email email@example.com for full details or to discuss how we can accommodate you).
This course is orientated to PhD and MSc students, as well as other students and researchers working on biogeography, spatial ecology, or related disciplines, with experience in ecological niche models.
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3ECT’s
Language – English
PLEASE READ – CANCELLATION POLICY: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact firstname.lastname@example.org. Failure to attend will result in the full cost of the course being charged.
Dr. Neftalí Sillero
Teaches – Ecological niche modelling using R; Advanced ecological niche modelling using RNeftalí Sillero works in the analysis and identification of biodiversity spatial patterns, from species to populations and individuals. For this, he uses four powerful tools to better understand how space influence biodiversity: Geographical Information Systems, Remote Sensing, Ecological Niche Modelling, and Spatial Statistics. His main areas of research are: application of new technologies on species’ distributions atlases, ecological modelling of species’ ranges, identification of biogeographical regions and species’ chorotypes, mapping and modelling road-kill hotspots, and spatial analyses of home ranges.
He has more than 10 years’ experience working in ecological niche models. He has authored >70 peer reviewed publications and he is since 2007 Chairman of the Mapping Committee of the Societas Herpetologica Europaea, where he is the PI of the NA2RE project (www.na2re.ismai.pt), the New Atlas of Amphibians and Reptiles of Europe.
Dr. Salvador Arenas-Castro
Teaches – Advanced ecological niche modelling using RSalvador Arenas-Castro works in the analysis of biodiversity spatial patterns and ecosystem dynamics, from the species to the ecosystem and landscape levels, according to forecasted environmental factors at different spatial and temporal scales. This approach constitutes a fundamental tool for improving biodiversity monitoring schemes for decision making. For that, his main research interests focus on spatial ecology, conservation biology, macroecology and biogeography. Overall, the main topics addressed have been focused on the analysis of ecological niche models, how biotic and abiotic factors, and other drivers, affect the dynamic and distribution of species, detect early warnings to support effective decisions on conservation policy and management in the face of global changes, and integrate the earth observation techniques into ecology and conservation biology for improving monitoring and conservation schemes. Additionally, to address his research questions, he has also used concepts and tools from different multidisciplinary scientific areas such as dendroecology, forest ecology, landscape ecology, remote sensing and GIS techniques applied to environmental sciences.
He has more than 6 years’ experience as postdoc in spatial ecology and biogeography. He is coauthor of 15 peer reviewed publications, collaborated in 9 research projects and contracts, coauthor of 8 technical reports, attendance to 12 National and International Scientific Congresses, and student supervisor in undergraduate and master degree.
The course will be mainly practical, with some theoretical lectures. All modelling processes and calculations will be performed with R, the free software environment for statistical computing and graphic(http://www.r-project.org/).
Assumed quantitative knowledge
A basic understanding of ecological niche models and biogeography in general is required.
Assumed computer background
Experience implementing ecological niche models using R is desirable.
Equipment and software requirements
A laptop/personal computer with a working version or R and RStudio installed. R and RStudio are supported by both PC and MAC and can be downloaded for free by following these links.
UNSURE ABOUT SUITABLILITY THEN PLEASE ASK email@example.com
Monday 25th – Classes from 09:30 to 17:30
- ENM guide: how to model.
- ENM R packages.
- Sources of environmental variables using dismo package.
- Getting species records with rgbif package.
Tuesday 26th – Classes from 09:30 to 17:30
- Variable selection with variance inflation factor (VIF) and usdm packages.
- Choosing the correct study area.
- Filtering records using usdm/sp Thin packages.
- Choosing pseudo-absences with Biomod2 package.
Wednesday 27th – Classes from 09:30 to 17:30
- Split records in training and test with ENMeval package.
- Test effect of Maxent regularization parameter.
- Comparing correlative models with AIC, with ENMeval package.
- Validate models null models.
Thursday 28th – Classes from 09:30 to 17:30
- MESS practice with Biomod2 package.
- VirtualSpecies SDMvspecies packages.
- MIGCLIM practice.
Friday 29th – Classes from 09:30 to 16:00
- Mechanistic model NicheMapper packages.
“PR-statistics offers a variety of courses, but ‘Introduction to Ecological Niche Modelling’ taught by an esteemed researcher of the field, Dr. Neftali Sillero, is definitely (either in their early in career or more experienced) a course any ecologist should attend.
The course started with a smooth and gentle introduction to the underlying principles of ecological niche modelling and provided a solid basis of how to build, test and evaluate an ecological niche model from start to finish. The instructor also took special care to point out which are the caveats you need to take care of when dealing with this kind of analysis. Dr. Sillero was always keen to answer our questions and attend to our needs and he even had time to discuss the problems we were facing with our own data (which ranged from plant/animal ecology to disease mapping).
It is an ideal course for anyone interested in species distribution modelling, either experienced or not, since it constitutes an extremely thorough and detailed step-by-step guide of how to approach the ever-growing ENM field. At least for me, it clarified a lot of concepts and I now feel confident about my modelling methodology.
Finally, Dr. Oliver Hooker, the heart and soul of PR-statistics, ensured that our stay in the Scottish Centre of Ecology and the Natural Environment (SCENE) would be as nice as possible and that we only had to worry about attending the lectures and nothing else. It was a memorable and fulfilling experience participating in the ENM course and I strongly recommend attending it.”
Kostas Kougioumoutzis, Ecologist
(Attended ENMR course)