Coding, data management, and Shiny applications using RStudio for evolutionary biologists and ecologists (CDSR01)
This course will run from the 15th - 19th May 2017 at SCENE field station, Loch Lomond, Scotland.
Course overview:
The course will introduce programming logic using the R syntax. The participants will be able to solve problems involving heterogeneous biological datasets and the combined use of different statistical packages, so the advantages of learning programming skills can be demonstrated. The RMarkdown syntax will be used to illustrate the advantages of literate programming and the possibilities of code sharing and archiving. In the sequence, participants will learn how to design relational databases (RDB) which can be used to manage and analyse large biological datasets. They will learn the basics of the SQL language and how to use it with R with the package {RMySQL}. To finalise, they will use the Shiny tool (R Studio) to build interactive applications to analyse and display data depending on user inputs. Throughout the course we will emphasise data, code and analyses best practices that could foster reproducibility and transparency in science, and the long-term availability of scientific data. At the end of the course the participants are expected to be able to develop small, tailored applications, to read and analyse datasets using a variety of statistics tools.
Intended Audience:
Researchers and postgraduate students working with in evolutionary biology and ecological data who want to have more autonomy and flexibility in their quantitative analyses, and need to access and analyse large datasets with R.
Day 1
Module 1: Programming Logic
- R syntax (Variable types - operators - conditionals - loops - writing functions)
- Programming and commenting code with RMarkdown
Day 2
Module 2: Data structures
- R syntax (arrays, lists, data frames, matrices)
- Data wrangling with {dplyr} and {tidyr}; the {ff} package and data tables for large datasets (e.g. transcriptomics; whole-genome data)
- Best practices of data acquisition, organization and storage
Day 3
Module 3: Relational databases
- Introduction to the SQL language and MySQL (open-source RDB freeware)
- Accessing and analysing large datasets using the package {RMySQL}
- As an example, we will combine DNA sequence datasets with IUCN Red List data illustrate the use of RDB to biological datasets.
Day 4
Module 4: Introduction to Shiny (R Studio)
- Shiny - Server and user interface commands
- As an example we will use Shiny to develop a small application where users can select different species and genes and run/visualize phylogenetic trees using {ape} running in the background.
Day 5
Module 5: Wrapping-up
- Development and presentation of individual projects combining data wrangling skills and user inputs using Shiny (R Studio)
Teaching Format:
The course will be highly practical, with a series of hands-on, step-by-step, problem-solving exercises, combining the different tools to solve ecological and evolutionary biology problems. The participants are invited to think of a problem that requires programming skills to be solved, and can bring their own data for a case-study. At the end of each day the participants will have time to work on their on projects and apply the skills learned on that day.
We offer two packages
COURSE ONLY - Includes lunch and refreshments.
ALL INCLUSIVE - Includes breakfast, lunch, dinner, refreshments, minibus to and from meeting point and accommodation. Accommodation is multiple occupancy (max 3 people) single sex en-suite rooms. Arrival Sunday 14th May and departure Friday 19th May PM.
Please send enquiries to oliverhooker@prstatistics.com or visit www.prstatistics.com for more details.
Other relevant upcoming 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 prstatistics.com facebook.com/prstatistics/ twitter.com/PRstatistics groups.google.com/d/forum/pr-statistics-post-course-forum prstatistics.com/organiser/oliver-hooker/
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