"Genetic data analysis/exploration using R" (GDAR03)
This course will be delivered by Dr. Thibaut Jombart who authors the adegenet package and Dr. Zhian Kamvar.
This course will run from the 23rd- 27th October at Margam discovery centre in Wales, United Kingdom.
Course Overview:
This course provides a comprehensive introduction to exploratory statistical methods used in population genetics and molecular ecology. Participants will become proficient in a range of approaches for uncovering genetic structures from usual genetic data including most genetic markers (e.g. microsatellites, SNPs, AFLP) and genetic sequences (DNA or amino-acid). After covering different types of phylogenetic reconstruction, and basic population genetics tests, a strong emphasis will be put on using factorial methods (e.g. Principal Component Analysis) for investigating genetic diversity. In particular, we will focus on the identification and description of genetic clusters, and on characterising spatial genetic patterns. The last day of the course will be an open problem day, where participants will be able to analyse their own data.
Day 1
Intro to phylogenetic reconstruction.
Module 1a: Reconstructing phylogenies from genetic sequence data. Three main approaches covered: distance-based phylogenies; maximum parsimony; and likelihood-based approaches.
Module 1b: Short R refresher.
Practical 1: Phylogenetic reconstruction using R. Three main approaches plus rooting a tree; assessing/testing for a molecular clock; and bootstrapping.
Main packages: ape, phangorn.
Day 2
Intro to multivariate analysis of genetic data
Module 2: Key concepts in multivariate analysis. Focus on using factorial methods for genetic data analysis.
Practical 2: Basics of multivariate analysis of genetic data in R. Topics include: data handling, population genetic tests of population structure (PCA, PCoA).
Main packages: adegenet, ade4, ape.
Day 3
Exploring group diversity
Module 3: Approaches to identifying and describing genetic clusters. Topics include: hierarchical clustering, K-means, population-level multivariate analysis (between-group-PCA, DA, DAPC).
Practical 3: Applying the approaches covered in morning lecture and emphasising their strengths and weaknesses.
Main packages: adegenet, ade4.
Day 4
Spatial genetic structures
Module 4: Discussing the origin and significance of spatial genetic patterns, and how to test for them.
Practical 4: Visualising and analysing spatial genetic data. Topics: spatial density estimates, Moran/Mantel tests, mapping principal components in PCA, spatial PCA.
Main packages: adegenet, adehabitat, ade4.
Day 5
Using R for reproducible science.
Module 5: Using R for reproducible science
Practical 5: Practical session based on morning lecture
Main packages: knitr, Sweave, rmarkdown
If you have any questions please email oliverhooker@prstatistics.com or visit www.prstatistics.com
To book online go to http://www.prstatistics.com/course/genetic-data-analysis-exploration-using-r-gdar03/
Other up-coming courses are as follows
ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R #MVSP 3rd - 7th April 2017, Scotland, Prof. Pierre Legendre, Dr. Olivier Gauthier http://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp02/
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/
CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS #CDSR 15th - 19th May, Scotland Dr. Aline Quadros http://www.prstatistics.com/course/coding-data-management-and-shiny-applications-using-rstudio-for-evolutionary-biologists-and-ecologists-cdsr01/
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/
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/
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/
BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS #BIGB 3rd - 7th July 2017, Scotland, Dr. Nic Blouin, Dr. Ian Misner http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/
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/
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/
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/
INTRODUCTION TO BIOINFORMATICS USING LINUX #IBUL 16th - 20th October, Scotland, Dr. Martin Jones http://www.prstatistics.com/course/introduction-to-bioinformatics-using-linux-ibul02/
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/
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/
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/
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/
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/
INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB 27th Nov - 1st Dec, Wales, Dr. Martin Jones http://www.prstatistics.com/course/introduction-to-python-for-biologists-ipyb04/
DATA VISUALISATION AND MANIPULATION USING PYTHON #DVMP 11th - 15th December 2017, Wales, Dr. Martin Jones http://www.prstatistics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/
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/
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/
ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME ??th - ??th February 2018, Wales, Dr Luca Borger, Dr. John Fieberg
AQUATIC TELEMENTRY DATA ANALYSIS USIR R (TBC) #ATDAR ??th - ??th February 2018, Wales,
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/
STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM Dr. Andrew Parnell, Dr. Andrew Jackson - Date and location to be confirmed
NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA Dr. Marco Scotti - Date and location to be confirmed
MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0 Prof David Warton - Date and location to be confirmed
ADVANCED PYTHON FOR BIOLOGISTS #APYB Dr. Martin Jones - Date and location to be confirmed
PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL Dr. Emmanuel Paradis - Date and location to be confirmed
Oliver Hooker PhD.
PR statistics
most recent publication - The physiological costs of prey switching reinforce foraging specialization - Journal of animal ecology - http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12632/full
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