[R-sig-genetics] Ecological niche modelling using R (ENMR03)

Wed Feb 6 22:54:41 CET 2019

Ecological niche modelling using R (ENMR03)

This course may be of interest to some list members although not fully
focused on genetics.

https://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr03/

This course will be delivered by Neftali Sillero form the 11th - 15th March
2019 in Glasgow City Centre.

Course Overview:
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.

Course programme:
Monday 11th – Classes from 09:30 to 17:30
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 12th – Classes from 09:30 to 17:30
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 13th – Classes from 09:30 to 17:30
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 14th – Classes from 09:30 to 17:30
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 15th – Classes from 09:30 to 16:00
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.

Email oliverhooker using prstatistics.com

Check out our sister sites,
www.PRstatistics.com (Ecology and Life Sciences)
www.PRinformatics.com (Bioinformatics and data science)
www.PSstatistics.com (Behaviour and cognition)

1. February 4th – 8th 2019
DESIGNING RELIABLE AND EFFICIENT EXPERIMENTS FOR SOCIAL SCIENCES (DRES01)
Glasgow, Scotland, Dr. Daniel Lakens
https://www.psstatistics.com/course/designing-reliable-and-effecient-experiments-for-social-sciences-dres01/

2. 25th February – 1st March 2019
MOVEMENT ECOLOGY (MOVE02)
Margam Discovery Centre, Wales, Dr. Luca Borger, Prof. Ronny Wilson, Dr
Jonathan Potts
https://www.prstatistics.com/course/movement-ecology-move02/

3. March 4th – 8th 2019
BIOACOUSTICS FOR ECOLOGISTS: HARDWARE, SURVEY DESIGN AND DATA ANALYSIS
(BIAC01)
Glasgow, Scotland, Dr. Paul Howden-Leach
https://www.prstatistics.com/course/bioacoustics-for-ecologists-hardware-survey-design-and-data-analysis-biac01/

4. March 11th – 15th  2019
ECOLOGICAL NICHE MODELLING USING R (ENMR03)
Glasgow, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr03/

5. March 18th – 22nd 2019
INTRODUCTION TO STATISTICS AND R FOR EVERYONE (IRFE01)
Athens, GREECE, Dr Aristides (Aris) Moustakas
https://www.prstatistics.com/course/introduction-to-statistics-and-r-for-anyone-irfe01/

6. March 25th – 29th 2019
LANDSCAPE GENETIC DATA ANALYSIS USING R (LNDG03)
Glasgow, Scotland, Prof. Rodney Dyer
http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg03/

7. April 1st – 5th 2019
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-ipsy02/

8. April 1st – 5th 2019
INDIVIDUAL BASED MODELS FOR ECOLOGSITS (IBME01)
Glasgow, Scotland, Dr Aristides (Aris) Moustakas
https://www.prstatistics.com/course/individual-based-models-using-r-and-netlogo-ibms01/

9. April 8th – 12th 2019
MACHINE LEARNING (MLUR01)
Glasgow, Scotland, Dr Aristides (Aris) Moustakas
https://www.prstatistics.com/course/machine-learning-using-r-mlur01/

10. April 15th – 19th 2019
INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB06)
Athens, GREECE,, Dr. Martin Jones
http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb07/

11. April 22nd – 26th 2019
GIS USING R (GISR)
Glasgow, Scotland, Dr Luca Nelli
https://www.prstatistics.com/course/gis-using-r-gisr01/

12. May 6th – 10th 2019
INTRODUCTION TO MULTILEVEL MODELS (MIXED/HIERARCHICAL) FOR PSYCHOLOGISTS
Myuna Bay, AUSTRALIA,  Dr. Sean Murphy
https://www.psstatistics.com/course/an-exploration-of-r-for-psychologists-from-data-handling-to-multilevel-modelling-xplr01/

13. May 16th – 19th 2019 (please note this a 4-day course from Thursday to
Monday)
INTRODUCTION TO R FOR EVERYONE (IRFE02)
Myuna Bay, AUSTRALIA, Dr Aristides (Aris) Moustakas
https://www.prstatistics.com/course/introduction-to-statistics-and-r-for-anyone-irfe02/

14. May 20th – 24th 2019
MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R (MBMV03)
Myuna Bay, AUSTRALIA, Prof. David Warton
https://www.prstatistics.com/course/model-based-multivariate-analysis-of-abundance-data-using-r-mbmv03/

15. May 21st – 24th 2019
STATISTICAL TOOLKIT FOR ECOLOGISTS (STKE01)
Myuna Bay, AUSTRALIA, Dr Aristides (Aris) Moustakas
https://www.prstatistics.com/course/statistical-toolkit-for-ecologists-stke01/

16. June 10th – 14th 2019
STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR (SIMM04)
Glasgow, Scotland, Dr. Andrew Parnell, Dr. Andrew Jackson
www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/

17. June 17th – 21st 2019
SPATIAL MODELLING AND ANALYSIS OF ADAPTIVE GENOMIC VARIATION (SPGN01)
Glasgow, Dr. Matt Fitzpatrick
https://www.prstatistics.com/course/spatial-modelling-and-analysis-of-adaptive-genomic-variation-spgn01/

18. June 17th – 21st 2019
INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB06)
Glasgow, Scotland, Dr. Martin Jones
http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb06/

19. June 24th – 28th 2019
ADVANCED PYTHON FOR BIOLOGISTS (APYB03)
Glasgow, Scotland, Dr. Martin Jones
www.prinformatics.com/course/advanced-python-biologists-apyb03/

20. July 1st – 5th 2019
DATA VISUALISATION AND MANIPULATION USING PYTHON (DVMP01)
Glasgow, Scotland, Dr. Martin Jones
http://www.prinformatics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/

21. July 29th – August 2nd 2019
INTRODUCTION TO SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (ISPE01)
Glasgow, Scotland, Dr. Jakub Nowosad
https://www.prstatistics.com/course/introduction-to-spatial-analysis-of-ecological-data-using-r-ispe01/

22. September 16th – 20th 2019
R PACKAGE DESIGN AND DEVELOPMENT AND REPRODUCIBLE DATA SCIENCE FOR
BIOLOGISTS (RPKG01)
Glasgow, Scotland, Dr. Cory Merow, Dr. Andy Rominger
https://www.prstatistics.com/course/r-package-design-and-development-and-reproducible-data-science-for-biologists-rpkg01/

23. September 30th – October 4th 2019
GEOMETRIC MORPHOMETRICS USING R (GMMR02)
Glasgow, Scotland, Prof. Dean Adams, Prof. Michael Collyer, Dr. Antigoni
Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr02/

24. October 7th – 11th 2019
CONSERVATION PLANNING USING PRIORITIZR : FROM THEORY TO PRACTICE (PRTZ01)
Athens, GREECE, Dr Richard Schuster and Nina Morell
https://www.prstatistics.com/course/conservation-planning-using-prioritizr-from-theory-to-practice-prtz01/

25. October 21st – 25th 2019
A COMPLETE GUIDE TO MIXED MODELS (INCLUDING TEMPORAL AND SPATIAL
AUTOCORRELATION) (MMTS01)
Athens, GREECE, Dr Aristides (Aris) Moustakas
https://www.prstatistics.com/course/a-complete-guide-to-mixed-models-including-temporal-and-spatial-autocorrelation-mmts01/

26. November 18th – 22nd 2019
INTRODUCTION TO STRUCTURED POPULATION MODELS AND DEMOGRAPHIC DISTRIBUTION
MODELS (IIPM01)
Athens, GREECE, Dr Cory Merow
https://www.prstatistics.com/course/introduction-to-structured-population-models-and-demographic-distribution-models-iipm01/

27. November 25th – 29th 2019
ADVANCED RANGE, NICHE, AND DISTRIBUTION MODELING (ASDM01)
Athens, GREECE, Dr Cory Merow
https://www.prstatistics.com/course/advanced-range-niche-and-distribution-modeling-asdm01/

-- 
Oliver Hooker PhD.
PR statistics

2018 publications -
Alternative routes to piscivory: Contrasting growth trajectories in brown
trout (Salmo trutta) ecotypes exhibiting contrasting life history
strategies. Ecology of Freshwater Fish.

Phenotypic and resource use partitioning amongst sympatric lacustrine brown
trout, Salmo trutta. Biological Journal of the Linnean Society. DOI
10.1093/biolinnean/bly032

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