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COURSE Quantitative geographic ecology using R: modelling genomes, niches, and communities


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#1 Melanie Colón

Melanie Colón
  • Moderators
  • 710 posts
  • Texas A&M University, College Station, TX,
  • United States

Posted 08 November 2017 - 08:57 AM

Quantitative geographic ecology using R: modelling genomes, niches, and
communities (QGER01)

https://www.prstatis...cology-using-r-
modelling-genomes-niches-and-communities-qger01/

30th April 2018 - 4th May 2018

Dr. Dan Warren and Dr. Matt Fitzpatrick

Course Overview:
Spatial modelling is increasingly being used in ecology and evolutionary
biology for both basic and applied research questions. While emphasis
traditionally has been on species-level niche modelling, the increasing
availability of genomic and community-level data has increased interest in
modelling biodiversity patterns above and below the species level. This
5-day course will provide a thorough introduction to different spatial
modelling techniques for quantifying and visualizing patterns of
biodiversity across scales of biological organization – from population-
level genetic variation, to species ecological niches, to communities.
Students will learn about theory, common data types, and statistical
techniques used in these different applications.

The course will include introductory lectures, guided computer coding in R,
and exercises for the participants, with an emphasis on visualization and
reproducible workflows. All modelling and data manipulation will be
performed with R. Attendees will learn to use niche modelling algorithms
including Maxent, GLM, GAM, and others, and will learn both new and
existing methods for conducting comparative studies using ENMs in the new
ENMTools R package.  Generalized Dissimilarity Modelling (GDM) and Gradient
Forest (GF) will be taught for modelling genomic and community-level data.
The course is intended for intermediate R users with interest in
quantitative geographical ecology.

After successfully completing this course students will:
1) Understand the theory underlying ENMs and the critical assumptions
necessary to the modelling process.
2) Be able to develop, evaluate, and apply ENMs both in the context of
conservation-oriented studies and to study niche evolution.
3) Understand the statistical underpinnings of GDM and GF
4) Be able to develop, evaluate and apply GDM and GF for quantifying and
mapping spatial genetic patterns and community-level compositional variation
5) Assess population- and community-level vulnerability to climate change

Monday 30th
Organisation and Introductions.
Spatial data in R.
Point data, vector data, and raster data.
GBIF, the Global Biodiversity Information Facility.
Interacting with Google Maps.
Working with raster and vector data.

Tuesday 1st
Ecological vs. historical biogeography.
ENM / SDM concepts and assumptions
Dismo
Conceptual and practical issues with ecological inferences from
distribution data.
Simulating species occurrence data.

Wednesday 2nd
Testing ecological and evolutionary hypotheses via Monte Carlo methods.
ENMTools R package.
Ecospat
Questions of taxonomic scale.
Incorporating niche conservatism into the modelling process.

Thursday 3rd
Introduction to community-level modeling
Background on GDM and GF
Review of data formats and data preparation
• Community-level data
• Genomic data
Model fitting and testing
Interpreting model results, including turnover functions
Model testing / validation / variable selection

Friday 4th
Predictions & Applications of GDM / GF
Transforming grids
Visualizing spatial variation in community / genetic composition
• Dissimilarity between locations
• Projecting patterns under climate change

Please send enquiries to oliverhooker@prstaititcs.com

Other upcoming courses

1.    November 6th – 10th 2017
LANDSCAPE GENETIC DATA ANALYSIS USING R #LNDG
Margam Discovery Centre, Wales, Prof. Rodney Dyer
http://www.prstatist...alysis-using-r-
lndg02/

2.    November 20th - 25th 2017
APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
SCENE, Scotland, Dr. Matt Denwood
http://www.prstatist...ing-ecologists-
epidemiologists-abme03/

3.    November 27th – December 1st 2017
INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
Margam Discovery Centre, Wales, Dr. Martin Jones
http://www.prinforma...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.prstatist...elling-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.prstatist...n-hierarchical-
modelling-using-r-ibhm02/

6.    January 29th – February 2nd 2018
PHYLOGENETIC DATA ANALYSIS USING R #PHYL
SCENE, Scotland, Dr. Emmanuel Paradis
https://www.prstatis...netic-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.prstatis...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.prstatist...using-r-gmmr01/
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9.    March 5th - 9th 2018
SPATIAL PRIORITIZATION USING MARXAN #MRXN
Margam Discovery Centre, Wales, Jennifer McGowan
https://www.prstatis...-marxan-mrxn01/

10.    March 12th - 16th 2018
ECOLOGICAL NICHE MODELLING USING R #ENMR
Glasgow, Scotland, Dr. Neftali Sillero
http://www.prstatist...elling-using-r-
enmr02/

11.    March 19th – 23rd 2018
BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKLIHOOD IN R #BDML
Glasgow, Scotland, Dr William Hoppitt
http://www.psstatist...-using-maximum-
likelihood-bdml01/
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12.    April 9th – 13th 2018
NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Glasgow, Scotland, Dr. Marco Scotti
https://www.prstatis...logists-ntwa02/

13.    April 16th – 20th 2018
INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R #IPSY
Glasgow, Scotland, Dr. Dale Barr, Dr Luc Bussierre
http://www.psstatist...cs-using-r-for-
psychologists-ipsy01/

14.    April 23rd – 27th 2018
MULTIVARIATE ANALYSIS OF ECOLOGICAL COMMUNITIES USING THE VEGAN PACKAGE
#VGNR
Glasgow, Scotland, Dr. Peter Solymos, Dr. Guillaume Blanchet
https://www.prstatis...-of-ecological-
communities-in-r-with-the-vegan-package-vgnr01/

15.    April 30th – 4th May 2018
QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND COMMUNITIES
#QGER
Glasgow, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick
https://www.prstatis...cology-using-r-
modelling-genomes-niches-and-communities-qger01/
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16.    May 7th – 11th 2018 ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL
ECOLOGICAL DATA USING R #MVSP
CANADA (QUEBEC), Prof. Pierre Legendre, Dr. Guillaume Blanchet
https://www.prstatis...al-analysis-of-
multivariate-ecological-data-theory-and-practice-mvsp03/

17.    May 14th - 18th 2018
INTRODUCTION TO MIXED (HIERARCHICAL) MODELS FOR BIOLOGISTS #IMBR
CANADA (QUEBEC), Prof Subhash Lele
https://www.prstatis...d-hierarchical-
models-for-biologists-using-r-imbr01/

18.    May 21st - 25th 2018
INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB
SCENE, Scotland, Dr. Martin Jones
http://www.prinforma...for-biologists-
ipyb05/

19.    May 21st - 25th 2018
INTRODUCTION TO REMOTE SENISNG AND GIS FOR ECOLOGICAL APPLICATIONS
Glasgow, Scotland, Prof. Duccio Rocchini, Dr. Luca Delucchi
https://www.prinform...ensing-and-gis-
for-ecological-applications-irms01/

20.    May 28th – 31st 2018
STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
CANADA (QUEBEC) Dr. Andrew Parnell, Dr. Andrew Jackson
https://www.prstatis...models-using-r-
simm04/

21.    May 28th – June 1st 2018
ADVANCED PYTHON FOR BIOLOGISTS #APYB
SCENE, Scotland, Dr. Martin Jones
https://www.prinform...logists-apyb02/
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22.    June 12th -0 15th 2018
SPECIES DISTRIBUTION MODELLING #DBMR
Myuna Bay sport and recreation, Australia, TBC
COMING SOON www.PRstatistics.com

23.    June 12th – 15th 2018
MARK RECAPTURE METHODS IN ECOLOGY #MKRC
Myuna Bay sport and recreation, Australia, TBC
COMING SOON www.PRstatistics.com

24.    June 18th – 22nd 2018
STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS
USING R #SEMR
Myuna Bay sport and recreation, Australia, TBC
COMING SOON www.PRstatistics.com
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25.    July 2nd - 5th 2018
SOCIAL NETWORK ANALYSIS FOR BEHAVIOURAL SCIENTISTS USING R #SNAR
Glasgow, Scotland, Prof James Curley
http://www.psstatist...for-behavioral-
scientists-snar01/

26.    July 8th – 12th 2018
MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV
Glasgow, Scotland, Prof David Warton
https://www.prstatis...te-analysis-of-
abundance-data-using-r-mbmv02/

27.    July 16th – 20th 2018
PRECISION MEDICINE BIOINFORMATICS: FROM RAW GENOME AND TRANSCRIPTOME DATA
TO CLINICAL INTERPRETATION #PMBI
Glasgow, Scotland, Dr Malachi Griffith, Dr. Obi Griffith
COMING SOON www.prinformatics.com

28.    July 23rd – 27th 2018
EUKARYOTIC METABARCODING
Glasgow, Scotland, Dr. Owen Wangensteen
http://www.prinforma...rcoding-eukb01/






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