Quantitative geographic ecology using R: modelling genomes, niches, and communities (QGER01)
This course will run from the 30th April - 4th May 2018 in Glasgow City Centre and is being delivered by Dr Dan Warren and Matt Fitzpatrick
Course Overview: 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 – Classes from 09:00 to 17:00 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 – Classes from 09:00 to 17:00 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 – Classes from 09:00 to 17:00 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 – Classes from 09:00 to 17:00 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 – Classes from 09:00 to 16:30 Predictions & Applications of GDM / GF Transforming grids Visualizing spatial variation in community / genetic composition • Dissimilarity between locations • Projecting patterns under climate change
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)
Please chare anywhere you see fit.
Email enquiries to firstname.lastname@example.org
Other up coming courses below
March 19th – 23rd 2018 BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKLIHOOD IN R (BDML01) Glasgow, Scotland, Dr William Hoppitt http://www.psstatistics.com/course/behavioural-data-analysis-using-maximum-likelihood-bdml01/
April 9th – 13th 2018 NETWORK ANAYLSIS FOR ECOLOGISTS USING R (NTWA02 Glasgow, Scotland, Dr. Marco Scotti
April 16th – 20th 2018 INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R (IPSY01) Glasgow, Scotland, Dr. Dale Barr, Dr Luc Bussierre
April 23rd – 27th 2018 MULTIVARIATE ANALYSIS OF ECOLOGICAL COMMUNITIES USING THE VEGAN PACKAGE (VGNR01) Glasgow, Scotland, Dr. Peter Solymos, Dr. Guillaume Blanchet
April 30th – 4th May 2018 QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND COMMUNITIES (QGER01) Glasgow, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick www.prstatistics.com/course/quantitative-geographic-ecology-using-r-modelling-genomes-niches-and-communities-qger01/
May 7th – 11th 2018 ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R (MVSP02) CANADA (QUEBEC), Prof. Pierre Legendre, Dr. Guillaume Blanchet www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp03/
May 14th - 18th 2018 INTRODUCTION TO MIXED (HIERARCHICAL) MODELS FOR BIOLOGISTS (IMBR01) CANADA (QUEBEC), Prof Subhash Lele www.prstatistics.com/course/introduction-to-mixed-hierarchical-models-for-biologists-using-r-imbr01/
May 21st - 25th 2018 INTRODUCTION TO PYTHON FOR BIOLOGISTS (IPYB05) SCENE, Scotland, Dr. Martin Jones http://www.prinformatics.com/course/introduction-to-python-for-biologists-ipyb05/
May 21st - 25th 2018 INTRODUCTION TO REMOTE SENISNG AND GIS FOR ECOLOGICAL APPLICATIONS (IRMS01) Glasgow, Scotland, Prof. Duccio Rocchini, Dr. Luca Delucchi www.prinformatics.com/course/introduction-to-remote-sensing-and-gis-for-ecological-applications-irms01/
May 28th – 31st 2018 STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR (SIMM04) CANADA (QUEBEC) Dr. Andrew Parnell, Dr. Andrew Jackson www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm04/
May 28th – June 1st 2018 ADVANCED PYTHON FOR BIOLOGISTS (APYB02) SCENE, Scotland, Dr. Martin Jones www.prinformatics.com/course/advanced-python-biologists-apyb02/
June 12th - 15th 2018 SPECIES DISTRIBUTION MODELLING (DBMR01) Myuna Bay sport and recreation, Australia, Prof. Jane Elith, Dr. Gurutzeta Guillera www.prstatistics.com/course/species-distribution-models-using-r-sdmr01/
June 18th – 22nd 2018 STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS USING R (SEMR02) Myuna Bay sport and recreation, Australia, Dr. Jon Lefcheck www.prstatistics.com/course/structural-equation-modelling-for-ecologists-and-evolutionary-biologists-semr02/
June 25th – 29th 2018 SPECIES DISTRIBUTION/OCCUPANCY MODELLING USING R (OCCU01) Glasgow, Scotland, Dr. Darryl McKenzie www.prstatistics.com/course/species-distributionoccupancy-modelling-using-r-occu01/
July 2nd - 5th 2018 SOCIAL NETWORK ANALYSIS FOR BEHAVIOURAL SCIENTISTS USING R (SNAR01) Glasgow, Scotland, Prof James Curley http://www.psstatistics.com/course/social-network-analysis-for-behavioral-scientists-snar01/
July 8th – 12th 2018 MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R (MBMV02) Glasgow, Scotland, Prof David Warton www.prstatistics.com/course/model-base-multivariate-analysis-of-abundance-data-using-r-mbmv02/
July 16th – 20th 2018 PRECISION MEDICINE BIOINFORMATICS: FROM RAW GENOME AND TRANSCRIPTOME DATA TO CLINICAL INTERPRETATION (PMBI01) Glasgow, Scotland, Dr Malachi Griffith, Dr. Obi Griffith www.prinformatics.com/course/precision-medicine-bioinformatics-from-raw-genome-and-transcriptome-data-to-clinical-interpretation-pmbi01/
July 23rd – 27th 2018 EUKARYOTIC METABARCODING (EUKB01) Glasgow, Scotland, Dr. Owen Wangensteen http://www.prinformatics.com/course/eukaryotic-metabarcoding-eukb01/
October 8th – 12th 2018 INTRODUCTION TO SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (ISAE01) Glasgow, Scotland, Prof. Subhash Lele https://www.prstatistics.com/course/introduction-to-spatial-analysis-of-ecological-data-using-r-isae01/
October 15th – 19th 2018 APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (ABME Glasgow, Scotland, Dr. Matt Denwood, Emma Howard http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme04/
October 29th – November 2nd 2018 PHYLOGENETIC COMPARATIVE METHODS FOR STUDYING DIVERSIFICATION AND PHENOTYPIC EVOLUTION (PCME01) Glasgow, Scotland, Prof. Subhash Lele Dr. Antigoni Kaliontzopoulou https://www.prstatistics.com/course/phylogenetic-comparative-methods-for-studying-diversification-and-phenotypic-evolution-pcme01/
November 26th – 30th 2018 FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND COMPUTATION (FEER Glasgow, 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/
February 2018 TBC MOVEMENT ECOLOGY (MOVE02) Margam Discovery Centre, Wales, Dr Luca Borger, Dr Ronny Wilson, Dr Jonathan Potts www.prstatistics.com/course/movement-ecology-move01/
-- 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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