Ecological niche modelling using R (ENMR02)
Delivered by Dr. Neftali Sillero
http://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
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 making
this course highly relevant to people studying the distribution of
marine mammals.
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.
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 26th
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
Our other courses
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1. January 29th – February 2nd 2018
INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (IBHM02)
SCENE, Scotland, Dr. Andrew Parnell
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/
2. January 29th – February 2nd 2018
PHYLOGENETIC DATA ANALYSIS USING R (PHYL02)
SCENE, Scotland, Dr. Emmanuel Paradis
https://www.prstatistics.com/course/introduction-to-phylogenetic-analysis-with-r-phyg-phyl02/
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3. February 19th – 23rd 2018
MOVEMENT ECOLOGY (MOVE01)
Margam Discovery Centre, Wales, Dr Luca Borger, Dr Ronny Wilson, Dr
Jonathan Potts
https://www.prstatistics.com/course/movement-ecology-move01/
4. February 19th – 23rd 2018
GEOMETRIC MORPHOMETRICS USING R (GMMR01)
Margam Discovery Centre, Wales, Prof. Dean Adams, Prof. Michael Collyer,
Dr. Antigoni Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/
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5. March 5th - 9th 2018
SPATIAL PRIORITIZATION USING MARXAN (MRXN01)
Margam Discovery Centre, Wales, Jennifer McGowan
https://www.prstatistics.com/course/introduction-to-marxan-mrxn01/
6. March 12th - 16th 2018
ECOLOGICAL NICHE MODELLING USING R (ENMR02)
Glasgow, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr02/
7. March 19th – 23rd 2018
BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKLIHOOD IN R (BDML01)
Glasgow, Scotland, Dr William Hoppitt
http://www.psstatistics.com/course/behavioural-data-analysis-using-maximum-likelihood-bdml01/
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8. April 9th – 13th 2018
NETWORK ANAYLSIS FOR ECOLOGISTS USING R (NTWA02
Glasgow, Scotland, Dr. Marco Scotti
https://www.prstatistics.com/course/network-analysis-ecologists-ntwa02/
9. April 16th – 20th 2018
INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R (IPSY01)
Glasgow, Scotland, Dr. Dale Barr, Dr Luc Bussierre
http://www.psstatistics.com/course/introduction-to-statistics-using-r-for-psychologists-ipsy01/
10. April 23rd – 27th 2018
MULTIVARIATE ANALYSIS OF ECOLOGICAL COMMUNITIES USING THE VEGAN PACKAGE
(VGNR01)
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/
11. April 30th – 4th May 2018
QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND
COMMUNITIES (QGER01)
Glasgow, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick
https://www.prstatistics.com/course/quantitative-geographic-ecology-using-r-modelling-genomes-niches-and-communities-qger01/
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12. May 7th – 11th 2018 ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL
ECOLOGICAL DATA USING R (MVSP02)
CANADA (QUEBEC), Prof. Pierre Legendre, Dr. Guillaume Blanchet
https://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp03/
13. May 14th - 18th 2018
INTRODUCTION TO MIXED (HIERARCHICAL) MODELS FOR BIOLOGISTS (IMBR01)
CANADA (QUEBEC), Prof Subhash Lele
https://www.prstatistics.com/course/introduction-to-mixed-hierarchical-models-for-biologists-using-r-imbr01/
14. May 21st - 25th 2018
INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB05)
SCENE, Scotland, Dr. Martin Jones
http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb05/
15. May 21st - 25th 2018
INTRODUCTION TO REMOTE SENISNG AND GIS FOR ECOLOGICAL APPLICATIONS
(IRMS01)
Glasgow, Scotland, Prof. Duccio Rocchini, Dr. Luca Delucchi
https://www.prinformatics.com/course/introduction-to-remote-sensing-and-gis-for-ecological-applications-irms01/
16. May 28th – 31st 2018
STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR (SIMM04)
CANADA (QUEBEC) Dr. Andrew Parnell, Dr. Andrew Jackson
https://www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/
17. May 28th – June 1st 2018
ADVANCED PYTHON FOR BIOLOGISTS (APYB02)
SCENE, Scotland, Dr. Martin Jones
https://www.prinformatics.com/course/advanced-python-biologists-apyb02/
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18. June 12th - 15th 2018
SPECIES DISTRIBUTION MODELLING (DBMR01)
Myuna Bay sport and recreation, Australia, TBC
https://www.prstatistics.com/course/species-distribution-models-using-r-sdmr01/
19. June 18th – 22nd 2018
STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS
USING R (SEMR02)
Myuna Bay sport and recreation, Australia, TBC
https://www.prstatistics.com/course/structural-equation-modelling-for-ecologists-and-evolutionary-biologists-semr02/
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20. July 2nd - 5th 2018
SOCIAL NETWORK ANALYSIS FOR BEHAVIOURAL SCIENTISTS USING R (SNAR01)
Glasgow, Scotland, Prof James Curley
http://www.psstatistics.com/course/social-network-analysis-for-behavioral-scientists-snar01/
21. July 8th – 12th 2018
MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R (MBMV02)
Glasgow, Scotland, Prof David Warton
https://www.prstatistics.com/course/model-base-multivariate-analysis-of-abundance-data-using-r-mbmv02/
22. July 16th – 20th 2018
PRECISION MEDICINE BIOINFORMATICS: FROM RAW GENOME AND TRANSCRIPTOME
DATA TO CLINICAL INTERPRETATION (PMBI01)
Glasgow, Scotland, Dr Malachi Griffith, Dr. Obi Griffith
https://www.prinformatics.com/course/precision-medicine-bioinformatics-from-raw-genome-and-transcriptome-data-to-clinical-interpretation-pmbi01/
23. July 23rd – 27th 2018
EUKARYOTIC METABARCODING (EUKB01)
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/
3/1, 128 Brunswick Street
Glasgow
G1 1TF
+44 (0) 7966500340
--
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
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