Advanced Species Distribution Modelling (SDM’s) and Ecological Niche Modelling (ENM’s)
Learn advanced SDM and ENM techniques in R. Includes Maxent tuning, MESS and null models, and building mechanistic models and virtual species.
Duration: 5 Days, 8 hours per day
Next Date: December 1-5, 2025
Format: Live Online Format
Portugal (GMT) local time - All sessions will be recorded and made available to ensure accessibility for attendees across different time zones.
£480Registration Fee
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5.0
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- Overview
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Course Description
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; to test effect of Maxent regularization parameter in models performance; to validate models performance and accuracy; to perform MESS analysis, null models, and mechanistic models, as well as to build your “virtual species”.
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.
What You’ll Learn
During the course will cover the following:
- 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”.
Attendees will learn to use functions implemented in the packages “usdm”; “dismo”; “ENMEval”; “SDMvspecies”; “spThin”; and “NicheMapper” among others.
Course Format
Interactive Learning Format
Each day features a well-balanced combination of lectures and hands-on practical exercises, with dedicated time for discussing participants’ own data, time permitting.
Global Accessibility
All live sessions are recorded and made available on the same day, ensuring accessibility for participants across different time zones.
Collaborative Discussions
Open discussion sessions provide an opportunity for participants to explore specific research questions and engage with instructors and peers.
Comprehensive Course Materials
All code, datasets, and presentation slides used during the course will be shared with participants by the instructor.
Personalized Data Engagement
Participants are encouraged to bring their own data for discussion and practical application during the course.
Post-Course Support
Participants will receive continued support via email for 30 days following the course, along with on-demand access to session recordings for the same period.
Who Should Attend / Intended Audiences
This course is designed for PhD and MSc students, as well as other students and researchers in biogeography, spatial ecology, or related fields, who have solid experience with ecological niche models, a strong background in biogeography, and proficiency in both Geographical Information Systems and the R statistical package; as the course focuses exclusively on advanced methods, prior knowledge of running ecological niche models is assumed—those seeking an introduction are encouraged to attend our basic course at PRStatistics (www.prstats.org).
Equipment and Software requirements
A laptop or desktop computer with a functioning installation of R and RStudio is required. Both R and RStudio are free, open-source programs compatible with Windows, macOS, and Linux systems.
A working webcam is recommended to support interactive elements of the course. We encourage participants to keep their cameras on during live Zoom sessions to foster a more engaging and collaborative environment.
While not essential, using a large monitor—or ideally a dual-monitor setup—can significantly enhance your learning experience by allowing you to view course materials and work in R simultaneously.
All necessary R packages will be introduced and installed during the workshop. A comprehensive list of required packages will also be shared with participants ahead of the course to allow for optional pre-installation.
Dr. Neftalí Sillero
Neftalí is a spatial ecologist specialising in the analysis and identification of biodiversity patterns at multiple scales, from individual organisms to species and populations. His work leverages Geographical Information Systems (GIS), Remote Sensing, Ecological Niche Modelling, and Spatial Statistics to explore how space influences biodiversity dynamics.
His core research interests include species distribution modelling, biogeographical region identification, chorotype analysis, mapping road-kill hotspots, and spatial analysis of animal home ranges. Neftalí has more than a decade of experience in ecological niche modelling and has published over 70 peer-reviewed articles. He also leads large-scale biodiversity mapping initiatives in Europe.
Since 2007, he has served as Chair of the Mapping Committee of the Societas Herpetologica Europaea, where he leads the NA2RE project (New Atlas of Amphibians and Reptiles of Europe).
Education & Career
- 10 years of experience in spatial ecology and ecological niche modelling
- Chair of the Mapping Committee, Societas Herpetologica Europaea (since 2007)
- Principal Investigator of the NA2RE Project – New Atlas of Amphibians and Reptiles of Europe
Research Focus
Neftalí’s research investigates how spatial processes shape biodiversity patterns. He specialises in integrating environmental data, spatial analysis tools, and modelling frameworks to map and predict species distributions and ecological risk zones, such as road-kill hotspots.
Current Projects
- NA2RE – New Atlas of Amphibians and Reptiles of Europe
- Spatial analysis of road mortality hotspots in European amphibians and reptiles
- Identification of biogeographical regions and species chorotypes using advanced modelling techniques
Professional Consultancy
Neftalí advises international conservation initiatives and biodiversity mapping efforts, contributing methodological expertise in GIS, remote sensing, and spatial statistics.
Teaching & Skills
- Specialist in GIS, remote sensing, niche modelling, and spatial statistics
- Experienced in teaching spatial ecology and biodiversity modelling
- Active in promoting spatial tools for conservation planning and policy
Links
Dr. Salvador Arenas-Castro
Salvador is a broad-spectrum ecologist whose work integrates fundamental ecology, macroecology, and biogeography with applied fields such as climate adaptation and land-use management. His interdisciplinary approach also spans agroecology, forestry, spatial ecology, and ecoinformatics. A key feature of his research is the explicit incorporation of spatial processes using spatially explicit modelling, GIS, and remote sensing techniques.
Salvador’s work seeks to bridge ecological theory with real-world applications, often through advanced spatial analysis and modelling tools. He is particularly interested in how large-scale ecological patterns respond to climate and landscape change, and how this understanding can inform more sustainable environmental management.
Education & Career
- Broad-spectrum ecologist with interests in ecology, macroecology, biogeography, and land-use
- Active researcher in agroecology, forestry, and spatial modelling
- Developer of spatially explicit models using GIS and remote sensing
- Research affiliations and academic output available via personal and professional pages
Research Focus
Salvador’s research addresses spatial dynamics of ecological systems, using integrative frameworks to study biodiversity, landscape structure, and environmental change. His work applies spatial modelling to understand and manage ecological complexity across scales.
Current Projects
- Spatial modelling of biodiversity responses to climate and land-use changes
- Applications of remote sensing in agroecology and forestry
- Ecoinformatics and GIS-based analysis of landscape-level ecological processes
Professional Consultancy
Salvador contributes expertise in spatial ecology and modelling to multi-disciplinary projects on sustainable land use and biodiversity management.
Teaching & Skills
- Specialises in GIS, remote sensing, spatial ecology, and modelling techniques
- Experienced in interdisciplinary approaches linking ecological research to practical land management
- Promotes integrative and spatially aware ecological analysis
Links
Session 1– 01:30:00 – ENM guide: how to model
Session 2 – 01:30:00 – ENM R packages.
Session 3 – 01:30:00 – Sources of environmental variables using geodata package.
Session 4 – 01:30:00 – Getting species records with geodata package.
Session 5 – 01:30:00 – Variable selection with variance inflation factor (VIF) and usdm packages.
Session 6 – 01:30:00 – Choosing the correct study area.
Session 7 – 01:30:00 – Filtering records using usdm/spThin packages.
Session 8 – 01:30:00 – Choosing pseudo-absences with Biomod2 package.
Session 9 – 02:00:00 – Split records in training and test with ENMeval package.
Session 10- 02:00:00 – Test effect of Maxent regularization parameter.
Session 11- 02:00:00 – Comparing correlative models with AIC, with ENMeval package.
Session 12- 02:00:00 – MESS practice with Biomod2 package.
Session 13- 02:00:00 – Validate models null models.
Session 14- 02:00:00 – VirtualSpecies virtualspecies packages.
Session 15 – 03:00:00 – Mechanistic model NicheMapper packages I.
Session 16 – 03:00:00 – Mechanistic model NicheMapper packages II.
Testimonials
PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.
Rolando O. Santos
PhD Assistant Professor, Florida International University
Courses attended
SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07
Testimonials
PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.
Rolando O. Santos
PhD Assistant Professor, Florida International University
Courses attended
SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07
Testimonials
PRStats offers a great lineup of courses on statistical and analytical methods that are super relevant for ecologists and biologists. My lab and I have taken several of their courses—like Bayesian mixing models, time series analysis, and machine/deep learning—and we've found them very informative and directly useful for our work. I often recommend PRStats to my students and colleagues as a great way to brush up on or learn new R-based statistical skills.
Rolando O. Santos
PhD Assistant Professor, Florida International University
Courses attended
SIMM05, IMDL03, ITSA02, GEEE01 and MOVE07
Frequently asked questions
Everything you need to know about the product and billing.
When will I receive instructions on how to join?
You’ll receive an email on the Friday before the course begins, with full instructions on how to join via Zoom. Please ensure you have Zoom installed in advance.
Do I need administrator rights on my computer?
I’m attending the course live — will I also get access to the session recordings?
I can’t attend every live session — can I join some sessions live and catch up on others later?
I’m in a different time zone and plan to follow the course via recordings. When will these be available?
I can’t attend live — how can I ask questions?
Will I receive a certificate?
When will I receive instructions on how to join?
You’ll receive an email on the Friday before the course begins, with full instructions on how to join via Zoom. Please ensure you have Zoom installed in advance.
Do I need administrator rights on my computer?
I’m attending the course live — will I also get access to the session recordings?
I can’t attend every live session — can I join some sessions live and catch up on others later?
I’m in a different time zone and plan to follow the course via recordings. When will these be available?
I can’t attend live — how can I ask questions?
Will I receive a certificate?
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