[MARMAM] Spatial analysis of ecologcial data using R

Oliver Hooker oliverhooker at prstatistics.com
Mon Apr 24 11:35:02 PDT 2017


'Spatial analysis of ecological data using R'

Delivered by Prof. Jason Matthiopoulos, Dr. James Grecian

http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/

This course will run from 7th – 12th August 2017 at SCENE field 
station, Loch Lomond national park, Scotland

The course will cover the concepts and R tools that can be used to 
analyse spatial data in ecology covering elementary and advanced spatial 
analysis techniques applicable to both plants and animals. We will 
investigate analyses appropriate to transect (e.g. line surveys, 
trapping arrays), grid (e.g. occupancy surveys) and point data (e.g. 
telemetry) making this course very relevant to those studying marine 
mammals. The focal questions will be on deriving species distributions, 
determining their environmental drivers and quantifying different types 
of associated uncertainty. Novel methodology for generating predictions 
will be introduced. We will also address the challenges of applying the 
results of these methods to wildlife conservation and resource 
management and communicate the findings to non-experts.

Course content is as follows

Day 1: Elementary concepts
Module 1 Introductory lectures and practical; this will cover the key 
questions in spatial ecology, the main types of data on species 
distributions, concepts and challenges and different types of 
environmental data, concepts and challenges; useful concepts from 
statistics; Generalised Linear Models
Module 2 GIS tools in R: Types and structure of spatial objects in R, 
generating and manipulating spatial objects,
projections and transformations, cropping and masking spatial objects, 
extracting covariate data and other simple
GIS operations in R, optionally plotting simple maps

Day 2: Overview of basic analyses
Module 3 Density estimation, Spatial autocorrelation, Smoothing, Kernel 
Smoothers, Kriging, Trend-fitting (linear, generalised linear, 
generalised additive models)
Module 4 Habitat preference, Resource selection functions, MaxEnt: 
What’s it all about? Overview and caveats related to Niche models

Day 3: Challenging problems
Module 5 Analysing grid data, Poisson processes, Occupancy models, 
Use-availability designs
Module 6 Analysing telemetry data, Presence-only data, Spatial and 
serial autocorrelation, Partitioning variation by
mixed effects models

Day 4: Challenging problems
Module 7 Analysing transect data, Detection functions for point and line 
transects, Using covariates in transect models. Afternoon for catch up 
and/or excursion

Day 5: Challenging problems
Module 8 Advanced methods, Generalised Estimation Equations for 
difficult survey designs, Generalised additive
models for habitat preference, Dealing with boundary effects using soap 
smoothers, Spatial point processes with INLA

Day 6: Delivering advice
Module 9 Prediction, Validation by resampling, Generalised Functional 
Responses for species distribution, Quantifying uncertainty, Dealing 
with the effects of population density
Module 10 Applications, designing protected areas, thinking about 
critical habitat, Representing uncertainty

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.	1.	ADVANCING IN STATISTICAL MODELLING FOR EVOLUTIONARY BIOLOGISTS AND 
ECOLOGISTS USING R #ADVR
17th – 21st April 2017, Scotland, Dr. Luc Bussiere, Dr. Ane Timenes 
Laugen
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr06/

2.	MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA #MASE
19th – 23rd June, Canada, Prof. Subhash Lele, Dr. Peter Solymos
http://www.prstatistics.com/course/multivariate-analysis-of-spatial-ecological-data-using-r-mase01/

3.	TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 #TSME
26th – 30th June, Canada, Dr. Andrew Parnell
http://www.prstatistics.com/course/time-series-models-foe-ecologists-tsme01/

4.	META-ANALYSIS IN ECOLOGY, EVOLUTION AND ENVIRONMENTAL SCIENCES 
#METR01
24th – 28th July, Scotland, Prof. Julia Koricheva, Prof. Elena 
Kulinskaya
http://www.prstatistics.com/course/meta-analysis-in-ecology-evolution-and-environmental-sciences-metr01/

5.	SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R #SPAE
7th – 12th August 2017, Scotland, Prof. Jason Matthiopoulos, Dr. James 
Grecian
http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/

6.	ECOLOGICAL NICHE MODELLING USING R #ENMR
16th – 20th October 2017, Scotland, Dr. Neftali Sillero
http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/

7.	GENETIC DATA ANALYSIS AND EXPLORATION USING R #GDAR
23rd – 27th October, Wales, Dr. Thibaut Jombart, Zhian Kavar
http://www.prstatistics.com/course/genetic-data-analysis-exploration-using-r-gdar03/

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

9.	LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG
6th – 10th November, Wales, Prof. Rodney Dyer
http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg02/

10.	APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME
20th - 25th November 2017, Scotland, Prof. Jason Matthiopoulos, Dr. Matt 
Denwood
http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/

11.	INTRODUCTION REMOTE SENSING AND GIS APPLICATIONS FOR ECOLOGISTS 
#IRMS
27th Nov – 1st Dec, Wales, Dr Duccio Rocchini, Dr. Luca Delucchi
http://www.prstatistics.com/course/introduction-to-remote-sensing-and-gis-for-ecological-applications-irms01/

12.	ADVANCING IN STATISTICAL MODELLING USING R #ADVR
11th – 15th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, 
Dr. Ane Timenes Laugen,
http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/

13.	INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM
29th Jan – 2nd Feb 2018, Scotland, Dr. Andrew Parnell
http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/

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

15.	GEOMETRIC MORPHOMETRICS USING R #GMMR
5th – 9th June 2017, Scotland, Prof. Dean Adams, Prof. Michael 
Collyer, Dr. Antigoni Kaliontzopoulou
http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/

16.	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.prstatistics.com/course/functional-ecology-from-organism-to-ecosystem-theory-and-computation-feer01/

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

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

19.	NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Dr. Marco Scotti - Date and location to be confirmed

20.	MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0
Prof David Warton - Date and location to be confirmed

21.	PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL
Dr. Emmanuel Paradis – Date and location to be confirmed


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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