[R-sig-genetics] PART FUNDED SCHOLARSHIPS - Coding, data management, and Shiny applications using RStudio for evolutionary biologists and ecologists - May 2017

Tue Apr 11 16:16:47 CEST 2017

PR STATISTICS ARE PLEASED TO ANNOUNCE THAT THROUGH THEIR FUNDING SCHEME 
THEY CAN OFFER 5 PART-FUNDED SCHOLARSHIPS FOR OUR UP-COMING COURSE

“Coding, data management, and Shiny applications using RStudio for 
evolutionary biologists and ecologists (CDSR01)"

SCHOLARSHIPS CONTRIBUTE TOWARDS TUITION FEES AND ACCOMMODATION WITH 5 
‘ALL INCLUSIVE PLACES’ AVAILABLE AT £490.00 (Fees have been 
subsidised by 35% from £755.00).

Applications should be sent to oliverhooker at prstatistics.com and contain
the following.
1.	Full name
2.	Institute name
3.	PhD subject title or Post doc research questions
4.	Do you hold a funded position
5.	150 words why this course would be relevant to your research or how 
it would help.

Application deadline is Tuesday 17th April 2017

We still have ‘normal’ places available for anyone else interested.

Full course details are given below

http://www.prstatistics.com/course/coding-data-management-and-shiny-applications-using-rstudio-for-evolutionary-biologists-and-ecologists-cdsr01/

This course will run from 15th - 19th May at SCENE field station, 
Scotland.

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.

Monday 15th
Module 1: Programming Logic
R syntax (Variable types – operators – conditionals – loops – 
writing functions)
Programming and commenting code with RMarkdown

Tuesday 16th
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
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
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
Module 5: Wrapping-up
Development and presentation of individual projects combining data 
wrangling skills and user inputs using Shiny (R Studio)

Please feel free to distribute this material anywhere you feel is 
suitable.

Upcoming courses - email for details oliverhooker at prstatistics.com

1.	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/

2.	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/

3.	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/

4.	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/

5.	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/

6.	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/

7.	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/

8.	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/

9.	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/

10.	INTRODUCTION TO BIOINFORMATICS USING LINUX #IBUL
16th – 20th October, Scotland, Dr. Martin Jones
http://www.prstatistics.com/course/introduction-to-bioinformatics-using-linux-ibul02/

11.	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/

12.	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/

13.	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/

14.	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/

15.	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/

16.	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/

17.	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/

18.	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/

19.	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/

20.	ANIMAL MOVEMENT ECOLOGY (February 2018) #ANME
19th - 23rd February 2018, Wales, Dr Luca Borger, Dr. John Fieberg

21.	AQUATIC TELEMENTRY DATA ANALYSIS USIR R (TBC) #ATDAR
??th - ??th February 2018, Wales,

22.	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/

23.	ADVANCES IN MULTIVARIATE ANALYSIS OF SPATIAL ECOLOGICAL DATA USING R 
#MVSP
Prof. Pierre Legendre, Dr. Olivier Gauthier - Date and location to be 
confirmed

24.	STABLE ISOTOPE MIXING MODELS USING SIAR, SIBER AND MIXSIAR #SIMM
Dr. Andrew Parnell, Dr. Andrew Jackson – Date and location to be 
confirmed

25.	NETWORK ANAYLSIS FOR ECOLOGISTS USING R #NTWA
Dr. Marco Scotti - Date and location to be confirmed

26.	MODEL BASE MULTIVARIATE ANALYSIS OF ABUNDANCE DATA USING R #MBMV0
Prof David Warton - Date and location to be confirmed

27.	ADVANCED PYTHON FOR BIOLOGISTS #APYB
Dr. Martin Jones - Date and location to be confirmed

28.	PHYLOGENETIC DATA ANALYSIS USING R (TBC) #PHYL
Dr. Emmanuel Paradis – 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.

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