Introduction to using R

15/08/2011

Would you too like to move into the R environment, but need a push over the threshold? This course will introduce the basics of R with lectures and hands-on exercises, led by Professor Uwe Ligges from University of Dortmund, and member of the R core development team. The course will focus on common statistics and graphics, while specialised packages of phylogenetics etc. is for you to explore after this week of intense R training.

The use of statistics should be essential to any biologist. For many years, many people have used specialized statistics software, with the advantages of a well developed graphical user interface, but with drawbacks such that they are often expensive and inflexible. In recent years, alternative free software have grown stronger in the market. The R software was first presented in 1993, and made available under the GNU General Public License in 1995. R is a software firstly developed for statistics and graphics, but since development is free to anyone, a large community of R users have developed tools which are specialised to their needs. At present, there are more than 1,000 packages available for R, of which several for genetics, phylogenetics etc. The use of R for publications within biology has increased a lot over the last decade, and is likely to continue to grow as the R project grows.

This course is co-organized by GENECO (www.geneco.se ), ClimBEco (www.cec.lu.se/graduate-research-school ) and CAnMove (http://canmove.lu.se ) at Lund University.

Course Outline

The course will run Monday to Thursday 9 am to 5 pm, and Friday 9 am to 1 pm. It will be an intensive course with a full schedule, featuring both lectures and a lot of practical exercises. Students are encouraged to use their own laptops, but some laptops will be available for lending.

Application

Apply at the latest October 1st via the GENECO homepage (http://www.geneco.se/Courses/Apply-to-course-courses ). State clearly if you are affiliated with GENECO, ClimBEco, or CAnMove, all which are allowed 10 participants each. The maximum total number of participants is 40.

Prerequisites and Course material

No formal prerequisites are required. We advise those who have not taken a statistics course on post-graduate level to do so, e.g. the PhD course Statistics for Biologists (http://www.biol.lu.se/o.o.i.s/27664 ), which runs immediately before the R course. The R course is open to PhD students, post-docs and senior scientists.

Course Coordinator

Martin Stervander

Dept. of Biology, Lund University

martin.stervander@biol.lu.se

046-222 37 06

Note absence 7 July–20 August and 3 September–20 October; please direct urgent questions to course administration during these periods.

Course Administration

Åsa Langefors

GENECO Research School

asa.langefors@biol.lu.se

046-2227921

Preliminary schedule: Introduction to using R

Course period: 12–16 December 2011.

A more detailed schedule will be presented later, below is the intended outline:

Section 1

Introduction (what is R?, history, R as a pocket calculator)
Data structures and data types
Data Import / Export

Section 2

if/else // loops, *apply
Functions, Scoping Rules, Debugging
Efficiency

Section 3

Simulations
Statistical Distributions
Graphics in R (base + lattice)
R packages

Section 4

Statistics in R (Linear models, Classification methods)
Object Oriented Programming Principles
Extensions (Compiled code, Namespaces, ...)