Ecological niche modelling using R (ENMR01=2) Delivered by Dr. Neftali Sillero
https://www.prstatistics.com/course/ecological-niche-modelling-using-r- enmr02/ This course will run from 12th – 16th March 2018 at SCENE field station, Loch Lomond national park, Scotland Applying niche modelling to the field of evolutionary biology has increased in recent years. It is especially important for field of ecological speciation, sympatric speciation, resource specialisation and studying how organisms and traits may evolve/cope with rapid changes to the environment such as those caused by climate change. 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 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. 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. Course content is as follows Monday 12th 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. Tuesday 13th 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. Wednesday 14th 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. Thursday 15th 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. Friday 16th 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. Please email any inquiries to oliverhoo...@prstatistics.com or visit our website www.prstatistics.com Please feel free to distribute this material anywhere you feel is suitable 1. November 6th – 10th 2017 LANDSCAPE GENETIC DATA ANALYSIS USING R #LNDG Margam Discovery Centre, Wales, Prof. Rodney Dyer http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r- lndg02/ 2. November 20th - 25th 2017 APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME SCENE, Scotland, Dr. Matt Denwood http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists- epidemiologists-abme03/ 3. November 27th – December 1st 2017 INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB Margam Discovery Centre, Wales, Dr. Martin Jones http://www.prinformatics.com/course/introduction-to-python-for-biologists- ipyb04/ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------------------ 4. December 4th - 8th 2017 ADVANCING IN STATISTICAL MODELLING USING R #ADVR Margam Discovery Centre, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, Dr. Ane Timenes Laugen, http://www.prstatistics.com/course/advancing-statistical-modelling-using-r- advr07/ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------------------ 5. January 29t – February 2nd 2018 INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM SCENE, Scotland, Dr. Andrew Parnell http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical- modelling-using-r-ibhm02/ 6. January 29th – February 2nd 2018 PHYLOGENETIC DATA ANALYSIS USING R #PHYL SCENE, Scotland, Dr. Emmanuel Paradis https://www.prstatistics.com/course/introduction-to-phylogenetic-analysis- with-r-phyg-phyl02/ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------------------ 7. February 19th – 23rd 2018 MOVEMENT ECOLOGY #MOVE Margam Discovery Centre, Wales, Dr Luca Borger, Dr Ronny Wilson, Dr Jonathan Potts https://www.prstatistics.com/course/movement-ecology-move01/ 8. February 19th – 23rd 2018 GEOMETRIC MORPHOMETRICS USING R #GMMR Margam Discovery Centre, Wales, Prof. Dean Adams, Prof. Michael Collyer, Dr. Antigoni Kaliontzopoulou http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------------------ 9. March 5th – 9th 2018 FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND COMPUTATION #FEER Margam Discovery Centre, Wales, Dr. Francesco de Bello, Dr. Lars Götzenberger, Dr. Carlos Carmona http://www.prstatistics.com/course/functional-ecology-from-organism-to- ecosystem-theory-and-computation-feer01/ 10. March 5th - 9th 2018 SPATIAL PRIORITIZATION USING MARXAN #MRXN Margam Discovery Centre, Wales, Jennifer McGowan https://www.prstatistics.com/course/introduction-to-marxan-mrxn01/ 11. 12th - 16th March 2018 ECOLOGICAL NICHE MODELLING USING R #ENMR Glasgow, Scotland, Dr. Neftali Sillero http://www.prstatistics.com/course/ecological-niche-modelling-using-r- enmr02/ 12. March 19th – 23rd 2018 BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKLIHOOD IN R #BDML Glasgow, Scotland, Dr William Hoppitt COMING SOON www.PSstatistics.com ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------------------ 13. April 9th – 13th 2018 NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA Glasgow, Scotland, Dr. Marco Scotti https://www.prstatistics.com/course/network-analysis-ecologists-ntwa02/ 14. April 16th – 20th 2018 INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R #IPSY Glasgow, Scotland, Dr. Dale Barr, Dr Luc Bussierre COMING SOON www.PSstatistics.com 15. April 23rd – 27th 2018 MULTIVARIATE ANALYSIS OF ECOLOGICAL COMMUNITIES USING THE VEGAN PACKAGE #VGNR Glasgow, Scotland, Dr. Peter Solymos, Dr. Guillaume Blanchet https://www.prstatistics.com/course/multivariate-analysis-of-ecological- communities-in-r-with-the-vegan-package-vgnr01/ 16. April 30th – 4th May 2018 QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND COMMUNITIES #QGER Glasgow, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick COMING SOON www.PRstatistics.com ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------------------ 17. 7th – 11th May 2018 ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R #MVSP CANADA (QUEBEC), Prof. Pierre Legendre, Dr. Guillaume Blanchet 18. 14th - 18th May 2018 INTRODUCTION TO MIXED MODELS FOR BIOLOGISTS #IMBR CANADA (QUEBEC), Prof Subhash Lele 19. 21st - 25th May 2018 INTRODUCTION TO REMOTE SENISNG AND GIS FOR ECOLOGICAL APPLICATIONS Glasgow, Scotland, Prof. Duccio Rocchini, Dr. Luca Delucchi https://www.prinformatics.com/course/introduction-to-remote-sensing-and-gis- for-ecological-applications-irms01/ 20. 28th May – 1st June 2018 STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM CANADA (QUEBEC) Dr. Andrew Parnell, Dr. Andrew Jackson ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ------------------ 21. July 2nd - 5th 2018 SOCIAL NETWORK ANALYSIS FOR BEHAVIOURAL SCIENTISTS USING R #SNAR Glasgow, Scotland, Prof James Curley COMING SOON www.PSstatistics.com 22. 8th – 12th July 2018 MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV Glasgow, Scotland, Prof David Warton https://www.prstatistics.com/course/model-base-multivariate-analysis-of- abundance-data-using-r-mbmv02/ 23. 16th – 20th July 2018 TRANSCRIPTOME ANALYSIS, VISUALIZATION AND INTERPRETATION #TAVI Glasgow, Scotland, Dr Malachi Griffith, Dr. Obi Griffith COMING SOON www.prinformatics.com 24. 23rd – 27th July 2018 EUKARYOTIC METABARCODING Glasgow, Scotland, Dr. Owen Wangensteen http://www.prinformatics.com/course/eukaryotic-metabarcoding-eukb01/ -- Oliver Hooker PhD. PR statistics 2017 publications - Ecosystem size predicts eco-morphological variability in post-glacial diversification. Ecology and Evolution. In press. The physiological costs of prey switching reinforce foraging specialization. Journal of animal ecology. prstatistics.com facebook.com/prstatistics/ twitter.com/PRstatistics groups.google.com/d/forum/pr-statistics-post-course-forum prstatistics.com/organiser/oliver-hooker/ 6 Hope Park Crescent Edinburgh EH8 9NA +44 (0) 7966500340
