`Coding, data management, and Shiny applications using RStudio for`

`evolutionary biologists and ecologists (CDSR01)`

http://www.prstatistics.com/course/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.`

Monday 15th – Classes from 09:00 to 17:00 Module 1: Programming Logic

`R syntax (Variable types – operators – conditionals – loops –`

`writing functions)`

Programming and commenting code with RMarkdown Tuesday 16th – Classes from 09:00 to 17:00 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 Wednesday 17th – Classes from 09:00 to 17:00 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.`

Thursday 18th – Classes from 09:00 to 17:00 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.`

Friday 19th – Classes from 09:00 to 16:00 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 oliverhoo...@prstatistics.com or visit`

`www.prstatistics.com for more details.`

Other relevant upcoming courses are as follows 1. ADVANCED PYTHON FOR BIOLOGISTS (February 2017) #APYB http://www.prstatistics.com/course/advanced-python-biologists-apyb01/

`2. STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR USING R`

`(February 2017) #SIMM`

http://www.prstatistics.com/course/stable-isotope-mixing-models-using-r-simm03/ 3. NETWORK ANAYLSIS FOR ECOLOGISTS USING R (March 2017) #NTWA http://www.prstatistics.com/course/network-analysis-ecologists-ntwa01/

`4. ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA (April`

`2017) #MVSP`

http://www.prstatistics.com/course/advances-in-spatial-analysis-of-multivariate-ecological-data-theory-and-practice-mvsp02/ 5. ADVANCING IN STATISTICAL MODELLING USING R (April 2017) #ADVR http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr06/

`6. CODING, DATA MANAGEMENT AND SHINY APPLICATIONS USING RSTUDIO FOR`

`EVOLUTIONARY BIOLOGISTS AND ECOLOGISTS (May 2017) #CDSR`

http://www.prstatistics.com/course/coding-data-management-and-shiny-applications-using-rstudio-for-evolutionary-biologists-and-ecologists-cdsr01/ 7. GEOMETRIC MORPHOMETRICS USING R (June 2017) #GMMR http://www.prstatistics.com/course/geometric-morphometrics-using-r-gmmr01/ 8. MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA (June 2017) #MASE http://www.prstatistics.com/course/multivariate-analysis-of-spatial-ecological-data-using-r-mase01/ 9. TIME SERIES MODELS FOR ECOLOGISTS USING R (JUNE 2017 (#TSME) 10. BIOINFORMATICS FOR GENETICISTS AND BIOLOGISTS (July 2017) #BIGB http://www.prstatistics.com/course/bioinformatics-for-geneticists-and-biologists-bigb02/ 11. SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R (August 2017) #SPAE http://www.prstatistics.com/course/spatial-analysis-ecological-data-using-r-spae05/ 12. ECOLOGICAL NICHE MODELLING (October 2017) #ENMR http://www.prstatistics.com/course/ecological-niche-modelling-using-r-enmr01/ 13. INTRODUCTION TO BIOINFORMATICS USING LINUX (October 2017) #IBUL http://www.prstatistics.com/course/introduction-to-bioinformatics-using-linux-ibul02/ 14. GENETIC DATA ANALYSIS USING R (October 2017 TBC) #GDAR

`15. STRUCTURAL EQUATION MODELLING FOR ECOLOGISTS AND EVOLUTIONARY`

`BIOLOGISTS (October 2017) #SEMR`

`16. LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (November 2017`

`TBC) #LNDG`

http://www.prstatistics.com/course/landscape-genetic-data-analysis-using-r-lndg02/

`17. APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS`

`(November 2017) #ABME`

http://www.prstatistics.com/course/applied-bayesian-modelling-ecologists-epidemiologists-abme03/ 18. INTRODUCTION TO METHODS FOR REMOTE SENSING (November 2017) #IRMS 19. INTRODUCTION TO PYTHON FOR BIOLOGISTS (November 2017) #IPYB http://www.prstatistics.com/course/introduction-to-python-for-biologists-ipyb04/

`20. DATA VISUALISATION AND MANIPULATION USING PYTHON (December 2017)`

`#DVMP`

http://www.prstatistics.com/course/data-visualisation-and-manipulation-using-python-dvmp01/ 21. ADVANCING IN STATISTICAL MODELLING USING R (December 2017) #ADVR http://www.prstatistics.com/course/advancing-statistical-modelling-using-r-advr07/ 22. INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (January 2018) #IBHM http://www.prstatistics.com/course/introduction-to-bayesian-hierarchical-modelling-using-r-ibhm02/ 23. ANIMAL MOVEMENT ECOLOGY February 2018) #ANME 24. AQUATIC TELEMENTRY DATA ANALYSIS USIR R (February 2018) #ATDAR 25. PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL Oliver Hooker PhD. PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/ -- Oliver Hooker PhD. PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/