Course on "Reproducible data science for population genetics" (RDPG01)
This course will be delivered by Dr. Thibaut Jombart who authors theadegenet package and Dr. Zhian Kamvar. www.prstatistics.com/course/reproducible-data-science-for-population- genetics-rdpg01/ This course will run from the 23rd - 27th October at Margam discovery centre in Wales, United Kingdom. Course Overview: With the increasing availability of various types of genetic and genomic data, population genetics and molecular ecology are becoming largely data driven sciences. Understanding the evolutionary, demographic, and ecological underpinning the genetic makeup of natural populations now relies on a combination of exploratory approaches and models. This course will provide an in-depth introduction to these techniques, with a strong emphasis on reproducibility though the use of modern analytic practices and tools. After an introduction to phylogenetic reconstruction, the course will cover a number of multivariate approaches for the analysis of genetic patterns, including supervised and unsupervised factorial methods, clustering approaches, and advanced methods for describing population diversity and revealing spatial genetic patterns. The approaches introduced will be applicable to most genetic data, including markers such as microsatellites, SNPs, or AFLP, as well as nucleotide and amino-acid sequence data. Every day will start with a lecture dedicated to a type of problem and methods, followed by an introduction to a specific technique for reproducible data analysis; afternoon will be devoted to hands on praticals. The last day will be devoted to open problems, where participants will be able to analyse their own data. Monday 23rd – Classes from 09:00 to 17:00 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: reproducible data science using R: an introduction Practical 1: phylogenetic reconstruction using R. Three main approaches plus rooting a tree; assessing/testing for a molecular clock; and bootstrapping. Main packages: knitr, ape, phangorn. Tuesday 24th – Classes from 09:00 to 17:00 Introduction to multivariate analysis of genetic data Module 2a: key concepts in multivariate analysis. Focus on using factorial methods for genetic data analysis. Module 2b: using R to generate high-quality pdf or word documents. Practical 2: multivariate analysis of genetic data in R. Topics include: data handling, Hardy-Weinberg tests, measures of diversity, tests of population structure, principal component analysis (PCA), multidimensional scaling (MDS). Main packages: knitr, rmarkdown, adegenet, ade4, pegasa, hierfstat, ape. Wednesday 25th – Classes from 09:00 to 17:00 Exploring group diversity Module 3a: approaches for identifying and describing genetic clusters. Topics include: hierarchical clustering, K-means, genetic distances between populations, supervised factorial methods including between-group PCA and the Discriminant Analysis of Principal Components (DAPC). Module 3b: using R to generate beamer and html5 slides. Practical 3: applying the approaches covered in morning lecture and emphasising their strengths and weaknesses. Main packages: rmarkdown, adegenet, ade4, hierfstat. Thursday 26th – Classes from 09:00 to 17:00 Spatial genetic structures Module 4a: on the origins of spatial genetic patterns, how to test for them, and how to reveal and visualise them. Module 4b: asking questions the right way with reproducible code. Practical 4: visualising and analysing spatial genetic data. Topics: spatial density estimates, univariate and multivariate tests of spatial structure (Moran and Mantel tests), mapping principal components from unsupervised methods (PCA), spatial PCA. Main packages: reprex, adegenet, spdep, ade4. Friday 27th – Classes from 09:00 to 16:00 Reproducible data science for population genetics in practice Open problem day – analyse your own data using R Main packages: knitr, rmarkdown, adegenet, ade4, ape, pegas, phangorn, hierfstat, poppr, ggplot2, etc. If you have any questions please email oliverhoo...@prstatistics.com or visit www.prstatistics.com www.prstatistics.com/course/reproducible-data-science-for-population- genetics-rdpg01/ Other up-coming courses are as follows 1. ECOLOGICAL NICHE MODELLING USING R #ENMR 16th – 20th October 2017, SCENE, Scotland, Dr. Neftali Sillero http://www.prstatistics.com/course/ecological-niche-modelling-using-r- enmr01/ 2. INTRODUCTION TO BIOINFORMATICS USING LINUX #IBUL 16th – 20th October, SCENE, Scotland, Dr. Martin Jones https://www.prinformatics.com/course/introduction-to-bioinformatics-using- linux-ibul02/ 3. REPRODUCIBLE DATA SCIENCE FOR POPULATION GENETICS #RDPG 23rd – 27th October 2017, Wales, Dr. Thibaut Jombart, Zhian Kavar https://www.prstatistics.com/course/reproducible-data-science-for- population-genetics-rdpg01/ 4. STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY BIOLOGISTS USING R #SEMR 23rd – 27th October 2017, Wales, Prof Jarrett Byrnes, Dr. Jon Lefcheck http://www.prstatistics.com/course/structural-equation-modelling-for- ecologists-and-evolutionary-biologists-semr01/ 5. LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R #LNDG 6th – 10th November 2017, Wales, Prof. Rodney Dyer http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r- lndg02/ 6. APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS #ABME 20th - 25th November 2017, SCENE, Scotland, Dr. Matt Denwood http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists- epidemiologists-abme03/ 7. INTRODUCTION TO PYTHON FOR BIOLOGISTS #IPYB 27th Nov – 1st Dec, Wales, Dr. Martin Jones http://www.prinformatics.com/course/introduction-to-python-for-biologists- ipyb04/ 8. ADVANCING IN STATISTICAL MODELLING USING R #ADVR 4th - 8th December 2017, Wales, Dr. Luc Bussiere, Dr. Tom Houslay, Dr. Ane Timenes Laugen, http://www.prstatistics.com/course/advancing-statistical-modelling-using-r- advr07/ 9. INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING #IBHM 29th Jan – 2nd Feb 2018, SCENE, Scotland, Dr. Andrew Parnell http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical- modelling-using-r-ibhm02/ 10. PHYLOGENETIC DATA ANALYSIS USING R #PHYL 28th Jan – Feb 2nd 2018, SCENE, Scotland, Dr. Emmanuel Paradis https://www.prstatistics.com/course/introduction-to-phylogenetic-analysis- with-r-phyg-phyl02/ 11. MOVEMENT ECOLOGY #MOVE 19th – 23rd February 2018, Wales, Dr Luca Borger, Dr Ronny Wilson, Dr Jonathan Potts https://www.prstatistics.com/course/movement-ecology-move01/ 12. GEOMETRIC MORPHOMETRICS USING R #GMMR 19th – 23rd February 2018, Wales, Prof. Dean Adams, Prof. Michael Collyer, Dr. Antigoni Kaliontzopoulou http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/ 13. FUNCTIONAL ECOLOGY FROM ORGANISM TO ECOSYSTEM: THEORY AND COMPUTATION #FEER 5th – 9th March 2018, SCENE, 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/ 14. SPATIAL PRIORITIZATION USING MARXAN #MRXN 5th - 9th March 2018, Wales, Jennifer McGowan https://www.prstatistics.com/course/introduction-to-marxan-mrxn01/ 15. ECOLOGICAL NICHE MODELLING USING R #ENMR 12th - 16th March 2018, SCENE, Scotland, Dr. Neftali Sillero http://www.prstatistics.com/course/ecological-niche-modelling-using-r- enmr02/ 16. BEHAVIOURAL DATA ANALYSIS USING MAXIMUM LIKLIHOOD IN R #BDML 19th – 23rd March 2018, Scotland, Dr William Hoppitt COMING SOON www.PSstatistics.com 17. NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA 9th – 13th April 2018, SCENE, Scotland, Dr. Marco Scotti https://www.prstatistics.com/course/network-analysis-ecologists-ntwa02/ 18. INTRODUCTION TO STATISTICAL MODELLING FOR PSYCHOLOGISTS USING R #IPSY 16th – 20th April 2018, SCENE, Scotland, Dr. Dale Barr, Dr Luc Bussierre COMING SOON www.PSstatistics.com 19. MULTIVARIATE ANALYSIS OF ECOLOGICAL COMMUNITIES USING THE VEGAN PACKAGE #VGNR 23rd – 27th April 2018, SCENE, Scotland, Dr. Peter Solymos, Dr. Guillaume Blanchet https://www.prstatistics.com/course/multivariate-analysis-of-ecological- communities-in-r-with-the-vegan-package-vgnr01/ 20. QUANTITATIVE GEOGRAPHIC ECOLOGY: MODELING GENOMES, NICHES, AND COMMUNITIES #QGER 30th April – 4th May 2018, SCENE, Scotland, Dr. Dan Warren, Dr. Matt Fitzpatrick COMING SOON www.PRstatistics.com 21. INTRODUCTION TO MIXED MODELS FOR ECOLOGISTS #IMMR 14th - 18th May 2018, CANADA (QUEBEC) STILL to be confirmed, Prof Subhash Lele, Dr. Guillaume Blanchet 22. STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM 28th May – 1st June 2018, CANADA (QUEBEC) STILL to be confirmed Dr. Andrew Parnell, Dr. Andrew Jackson 23. SOCIAL NETWORK ANALYSIS FOR BEHAVIOURAL SCIENTISTS USING R #SNAR 2nd - 5th12th July 2018, Prof James Curley COMING SOON www.PSstatistics.com 24. MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV 8th – 12th July 2018, Prof David Warton https://www.prstatistics.com/course/model-base-multivariate-analysis-of- abundance-data-using-r-mbmv02/ 25. EUKARYOTIC METABARCODING 23rd – 27th July 2018, Wales, Dr. Owen Wangensteen http://www.prinformatics.com/course/eukaryotic-metabarcoding-eukb01/ 26. ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R #MVSP Prof. Pierre Legendre, Dr. Olivier Gauthier - 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. prstatistics.com facebook.com/prstatistics/ twitter.com/PRstatistics groups.google.com/d/forum/pr-statistics-post-course-forum prstatistics.com/organiser/oliver-hooker/ 3/1, 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340
