Advanced Course: R programming and development

• EMBL Heidelberg, 15 - 16 Jan 2015
• Course Details

Setup

A laptop with a recent R (>= 3.1.1), including developer tools (for Windows, this means Rtools). See here for installation details.

To test your R installation, try the following

## If you don't have devtools
install.packages("devtools")

library("devtools")
install_github("lgatto/sequences")

If you do not have any favourite editor, have a go with Rstudio.

Programme

Day 1

When	What
	Setup and welcome	LG
09:15 - 10:30	OO Introduction	RS
	Break
11:00 - 12:30	S3/S4 object-oriented programming	RS
	Lunch
13:30 - 15:30	Package development	RS
	Break
16:00 - 17:30	Advanced issues in package development and documentation	RS

To see a full implementation of the OO and package development material, see the sequences package (also on CRAN).

Day 2

Additional packages

install.packages(c("RUnit", "microbenchmark"))

library("BiocInstaller")
## if BiocInstaller is not installed
source("http://www.bioconductor.org/biocLite.R")
biocLite("BiocParallel")

install.packages("shiny")

## rauthoring dependencies
biocLite(c("knitr", "rmarkdown", "markdown", "ReportingTools", "DESeq2"))

library("devtools")
install_github("lgatto/rauthoring")

When	What
09:15 - 10:40	Testing, Unit testing and debugging	LG
	Break
11:00 - 12:30	Benchmarking, profiling and optimisation and calling C/C++ code	LG
	Lunch
13:30 - 15:30	Vectorisation, functional programming and parallelisation (src)	LG
	Break
15:50 - 17:30	R authoring and building web interfaces: shiny (vignettes in the rauthoring package)	LG
	Wrap up	all

Useful refs

• Various teaching material: https://github.com/lgatto/teachingmaterial
• Advanced R by Hadley Wickham
• Package development
• Bioconductor package development