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Ecological niche modelling using R (ENMR03R)

12 December 2022 - 15 December 2022

£360.00
Ecological niche modelling using R (ENMR03R)

Event Date

On Demand

Course Format

Pre Recorded

About This Course

The course will cover the base theory of ecological niche modelling and its main methodologies. By the end of this 5-day practical course, attendees will have the capacity to perform ecological niche models and understand their results, as well as to choose and apply the correct methodology depending on the aim of their type of study and data.

Ecological niche, species distribution, habitat distribution, or climatic envelope models are different names for similar mechanistic or correlative models, empirical or mathematical approaches to the ecological niche of a species, where different types of ecogeographical variables (environmental, topographical, human) are related with a species physiological data or geographical locations, in order to identify the factors limiting and defining the species’ niche. ENMs have become popular due to the need for efficiency in the design and implementation of conservation management.

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 graphics (http://www.r-project.org/). Attendees will learn to use modelling algorithms like Maxent, Bioclim, Domain, and logistic regressions, and R packages for computing ENMs like Dismo and Biomod2. Also, students will learn to compare different ecological niche models using the Ecospat package.

 

Intended Audiences

This course is orientated to PhD and MSc students, as well as persons in researcher or industry working on biogeography, spatial ecology, or related disciplines.

Course Details
Last Up-Dated 15:03:2019

Duration – Approx. 28 hours

ECT’s – Equal to 3 ECT’s

Language – English

Teaching Format
Introductory lectures on the concepts and applications of ENM. Practical lectures on most used ENM methods. Presentations and round-table discussions about the analysis requirements of attendees (option for them to bring their own data). Data sets for computer practicals will be provided by the instructor, but participants are welcome to bring their own data.
Assumed quantitative knowledge
Basic knowledge in Geographical Information Systems and spatial analyses.
Assumed computer background
Familiarity with GIS software like QGIS. Ability to visualise shapefiles and raster files. Familiarity with R. Ability to import/export data, manipulate data frames, fit basic statistical models & generate simple exploratory and diagnostic plots.
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

Tickets

The numbers below include tickets for this event already in your cart. Clicking "Get Tickets" will allow you to edit any existing attendee information as well as change ticket quantities.
ENMR03R PRE RECORDED
ENMR03R PRE RECORDED
£ 360.00
Unlimited

PLEASE READ – CANCELLATION POLICY

Cancellations/refunds are accepted as long as the course materials have not been accessed,.

There is a 20% cancellation fee to cover administration and possible bank fess.

If you need to discuss cancelling please contact oliverhooker@prstatistics.com.

If you are unsure about course suitability, please get in touch by email to find out more oliverhooker@prstatistics.com

 

COURSE PROGRAMME

Day 1
Day 1 – Approx. 7 hours

Elementary concepts on Ecological Niche Modelling

Module 1: Introduction to ENM theory. Definition of ecological niche model; introduction to species ecological niche theory, types of ecological niches, types of ENM, diagram BAM, ENMs as approximations to species’ niches.

Module 2: Problems and limitations on ENM. Assumptions and uncertainties, equilibrium concept, niche conservatism, autocorrelation and intensity, sample size, correlation of environmental variables, size and form of study area, thresholds, model validation, model projections.

Module 3: Methods on ENM. Mechanistic and correlative models. Overlap Analysis, Biomod, Domain, Habitat, Distance of Mahalanobis, ENFA, GARP, Maxent, Logistic regression, Generalised Linear Models, Generalised Additive Models, Generalised Boosted Regression Models, Random Forest, Support Vector Machines, Artificial Neural Network.

Module 4: Conceptual and practice steps to calculate ENM. How to make an ENM step-by-step.

Module 5: Applications of ENM. Ecological niche identification, Identification of contact zones, Integration with genetical data, Species expansions, Species invasions, Dispersion hypotheses, Species conservation status, Prediction of future conservation problems, Projection to future and past climate change scenarios, Modelling past species, Modelling species richness, Road-kills, Diseases, Windmills, Location of protected areas.

Day 2
Day 2 – Approx. 7 hours

Prepare environmental variables and run ecological niche models with dismo package.

Module 6: Preparing variables. Choosing environmental data sources, Downloading variables, Clipping variables, Aggregating variables, Checking pixel size, Checking raster limits, Checking NoData, Correlating variables.

Module 7: Dismo practice. How to run an ENM using the R package dismo.

 

Day 3
Day 3 – Approx. 7 hours

Run ecological niche models with Biomod2 package and Maxent.

Module 8: Biomod2 practice. How to run an ENM using the R package Biomod2.

Module 9: Maxent practice. How to run an ENM using the R packages dismo and Biomod2 as well as Maxent software.

Day 4
Day 4 – Approx. 7 hours

Compare ecological niche models with ecospat.

Module 10: Ecospat practice. Compare statistically two different ecological niche models using the R package Ecospat.

Module 11: Students’ talks. Attendees will have the opportunity to present their own data and analyse which is the best way to successfully obtain an ENM.

 

Day 5
Day 5 – Approx. 7 hours

Run ecological niche models with your own data.

Module 12: Final practical. In this practical, the students will run ENM with their own data or with a new dataset, applying all the methods showed during the previous days.

 

Dr. Neftali Sillero
Dr. Neftali Sillero

Neftalí 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

Personal website
Work Webpage
ResearchGate
GoogleScholar

Teaches
  • Ecological Niche Modelling Using R (ENMR)
  • Advanced Ecological Niche Modelling Using R (ANMR)
  • GIS And Remote Sensing Analyses With R (GARM)
Teaches
  • Ecological Niche Modelling Using R (ENMR)
  • Advanced Ecological Niche Modelling Using R (ANMR)
  • GIS And Remote Sensing Analyses With R (GARM)

Details

Start:
12 December 2022
End:
15 December 2022
Cost:
£360.00
Event Category:

Tickets

The numbers below include tickets for this event already in your cart. Clicking "Get Tickets" will allow you to edit any existing attendee information as well as change ticket quantities.
ENMR03R PRE RECORDED
ENMR03R PRE RECORDED
£ 360.00
Unlimited