[R-sig-eco] Repeat course on ecological niche modelling using R

Mon Oct 23 19:48:44 CEST 2017

Ecological niche modelling using R (ENMR02)

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 oliverhooker at 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/
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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/
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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/
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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/
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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
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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
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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
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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

-- 
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