Advanced Ecological Niche Modelling Using R (ANMR01)
12th October 2020 - 16th October 2020£275.00 - £550.00
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 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.
Venue – PR statistics head office, 53 Morrison Street, Glasgow, G5 8LB – Google Map
Availability – 24 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3ECT’s
Language – English
We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments and welcome meal Monday evening.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, refreshments and welcome dinner Monday evening. Self-catering facilities are available in the accommodation. Accommodation is approximately a 6-minute walk from the PR statistics head office. Accommodation is multiple occupancy (max 3-4 people) single sex en-suite rooms. Arrival Sunday 28th July (between 17:00-21:00) and departure Friday 2nd August(accommodation must be vacated by 09:15).
To book ‘COURSE ONLY’ with the option to add the additional ‘ACCOMMODATION PACKAGE’ please scroll to the bottom of this page.
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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. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees (and accommodation fees if booked through PR statistics) will be credited. However, PR statistics will not be held responsible/liable for any travel fees, accommodation costs or other expenses incurred to you as a result of the cancellation. Because of this PR statistics strongly recommends any travel and accommodation that is booked by you or your institute is refundable/flexible and to delay booking your travel and accommodation as close the course start date as economical viable.
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.
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Sunday 11th Meet at 43 Cook Street, Glasgow G5 8JN between 17:00-21:00 onwards
Monday 12th – 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 13th – 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 14th – 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 15th – Classes from 09:30 to 17:30
MESS practice with Biomod2 package.
VirtualSpecies SDMvspecies packages.
Friday 16th – 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)