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Multivariate analysis of ecological communities in R with the VEGAN package


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#1 Melanie Colón

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

Posted 20 September 2017 - 08:48 AM

Multivariate analysis of ecological communities in R with the VEGAN package
(VGNR01)

https://www.prstatis...-of-ecological-
communities-in-r-with-the-vegan-package-vgnr01/

Instructors:
Dr. Peter Solymos and Dr. Guillaume Blanchet

When:
23rd - 27th April 2018

Where:
SCENE filed station, Loch Lomond, Glasgow

Intended Audience:
Research postgraduates, practicing academics and primary investigators in
spatial ecology and management and environmental professionals in
government and industry.

Course Overview:
This 5-day course will cover the concepts, methods, and R tools that can be
used to analyse community ecology data. The course will review data
processing techniques relevant to multivariate data sets. We will cover
diversity and null-model analysis, distance measures and distance based
multivariate methods, clustering, classification, and dimension reduction
techniques using the vegan R extension package. We will use real world data
sets to motivate the analyses, e.g. describing patterns along environmental
or anthropogenic disturbance gradients, quantifying the effects of
continuous and discrete predictors, and making predictions based on
multivariate model results. We will emphasize visualization and
reproducible workflows. Modules will consist of introductory lectures,
guided computer coding, and exercises for the participants. The course is
intended for intermediate R users with interest in community ecology,
especially in the fields of terrestrial and wetland ecology, microbial
ecology, and natural resource management.

Course syllabus:
Monday 23rd – Classes from 08:30 to 16:30
Module 1: Introduction to community data analysis, basics of programming in
R
Module 2: Data processing (long and wide data representations, single and
multiple table operations, data aggregation and transformation)

Tuesday 24th – Classes from 08:30 to 16:30
Module 3: Diversity analysis, species-abundance distributions, null-model
analysis
Module 4: Distance measures and distance based methods (Mantel test,
distance decay, etc.)

Wednesday 25th – Classes from 08:30 to 16:30
Module 5: Hierarchical and nonhierarchical clustering and classification
Module 6: Dispersion and permutational MANOVA

Thursday 26th – Classes from 08:30 to 16:30
Module 7: Response curves, ordination (correspondence analysis, nonmetric
scaling, constrained ordination).
Module 8: Fitting environmental variables to ordination, permutation based
testing of the significance of constraints.

Friday 27th – Classes from 08:30 to 16:30
Module 9: Indicator species analysis and multivariate calibration.
Modules 10: special topics and discussion, analyzing participants’ own data.

If you have any questions please feel free to mail
oliverhooker@prstatistics.com or visit www.prstatisticas.com

Upcoming courses for 2017/2018 below

ECOLOGICAL NICHE MODELLING USING R #ENMR
16th – 20th October 2017, Scotland, Dr. Neftali Sillero
http://www.prstatist...elling-using-r-
enmr01/

2.    REPRODUCIBLE DATA SCIENCE FOR POPULATION GENETICS #RDPG
23rd – 27th October 2017, Wales, Dr. Thibaut Jombart, Zhian Kavar
https://www.prstatis...ta-science-for-
population-genetics-rdpg01/

3.    STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY
BIOLOGISTS USING R #SEMR
23rd – 27th October 2017, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck
http://www.prstatist...-modelling-for-
ecologists-and-evolutionary-biologists-semr01/

4.    LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG
6th – 10th November 2017, Wales, Prof. Rodney Dyer
http://www.prstatist...alysis-using-r-
lndg02/

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

6.    ADVANCING IN STATISTICAL MODELLING USING R #ADVR
11th – 15th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, Dr.
Ane Timenes Laugen,
http://www.prstatist...elling-using-r-
advr07/

7.    INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
29th Jan – 2nd Feb 2018, Scotland, Dr. Andrew Parnell
http://www.prstatist...n-hierarchical-
modelling-using-r-ibhm02/

8.    PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL
28th Jan – Feb 2nd 2018 Dr. Emmanuel Paradis
https://www.prstatis...netic-analysis-
with-r-phyg-phyl02/

9.    ANIMAL MOVEMENT ECOLOGY #ANME
19th – 23rd February 2018, Wales, Dr Luca Borger, Dr. John Fieberg

10.    GEOMETRIC MORPHOMETRICS USING R #GMMR
19th – 23rd February 2018, Scotland, Prof. Dean Adams, Prof. Michael
Collyer, Dr. Antigoni Kaliontzopoulou
http://www.prstatist...using-r-gmmr01/

11.    FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND
COMPUTATION #FEER
5th – 9th March 2018, Scotland, Dr. Francesco de Bello, Dr. Lars
Götzenberger, Dr. Carlos Carmona
http://www.prstatist...om-organism-to-
ecosystem-theory-and-computation-feer01/

12.    SPATIAL PRIORITIZATION USING MARXAN
5th - 9th March 2018, Wales, Jennifer McGowan
https://www.prstatis...-marxan-mrxn01/

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

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

15.    NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
9th – 13th April 2018, Scotland, Dr. Marco Scotti
https://www.prstatis...logists-ntwa02/

16.    QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND
COMMUNITIES
30th April – 4th May 2018, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick

17.    INTRODUCTION TO MIXED MODELS FOR ECOLOGISTS #IMMR
28th May – 1st June 2018, Canada, Prof Subhash Lele, Dr. Guillaume Blanchet

18.    MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0
8th – 12th July 2018, Prof David Warton
https://www.prstatis...te-analysis-of-
abundance-data-using-r-mbmv02/

19.    ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING
R #MVSP
Prof. Pierre Legendre, Dr. Olivier Gauthier - Date and location to be
confirmed

20.    STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
Dr. Andrew Parnell, Dr. Andrew Jackson – Date and location to be confirmed

21.    MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA #MASE
Prof. Subhash Lele, Dr. Peter Solymos - Date and location to be confirmed

22.    TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME
Dr. Andrew Parnell - Date and location to be confirmed

23.    SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #METR
Prof. Jason Matthiopoulos – Date and location to be confirmed

24.    META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES #METR
Prof. Julia Koricheva, Prof. Elena Kulinskaya – Date and location to be c

--
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.

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