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
