Program Overview

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Programming with R for Reproducible Research

Course Synopsis

The course provides an overview of programming with R for reproducible research.

Prerequisites

• Both parts of "Using R for Data Analysis" (lecture in fall semester), or similar knowledge of R on at least an intermediate level
  • Slides of "Using R .." (2013)
  • Slides of "Using R .." (2012) (with slightly more material in part 2)
  • The "textbook" of "Using R": Longhow Lam (2010). An Introduction to R freely available from CRAN.
• Laptop with R (>= 3.0.1) and one of RStudio / StatET / ESS, (or similar) "R IDE" installed. Two students may team up, using one computer.
• One semester of (introduction to) statistics

Start of Lectures

Tuesday, 23.02.2016

Lecture Material

Week 1

• Organization, Topics, etc: Emacs org (source), pdf.
• R code during browsing of "Using R.." chapter 7: -ex.R.
• R markdown ("Rmd") file first.Rmd, conveniently opened in Rstudio, demonstrating both R markdown with its HTML, i.e. web content output.
• "Everything (in R) is an object" --> explorations and a table and its Rmd source

Week 2

• Your questions about "Using R" (and the material above)
• && vs & and || vs |
• coercion:
• More on functions, notably closures: The 2 (and three) parts of a function: Commented R code and R markdown.
• Excursion: Exploring R packages and functions in there:
• Using the R code from Matloff's book.

Week 3

• Our edition of original Ch7/bookvec.R
• our example "text corpus" text1.txt
• Our version of original Ch4/findwords.R; and the (more efficient!)
• Our modified excerpt of H.Wickham's functional programming chapter.

Week 4

• continuing "functional programming" (week 3, above)
• The initial R session, somewhat extended, of How R Searches and Finds Stuff
• Functions -> environments:
• ls(), get(), assign(), find(), ls.str(), new.env(), parent.env(),
• globalenv(), emptyenv(), and the first two figures in How R Searches and Finds Stuff

Week 5

• one_counter() example in "functional programming" (above) --- please study as , ask in class.
• "R is slow" etc:
  • "Premature optimization is the root of all evil ", Donald Knuth
  • Rather: Test, test, and test again; using all.equal(target, current, tolerance ~= 10^-8)
  • typical issue about for() loop from Stackoverflow
  • User Q about 'matrix vs. data.frame' on the R-help mailing list (March 2014).
  • Our (modified) Rmd on "Performance" from Hadley Wickham's book chapter "Performance".

Week 6

• Continuing "Performance" (see week 5): "Measure, don't guess" --> Using Rprof() and microbenchmark
• The 'matrix vs. data.frame' R-help example continued see above).
• R's byte compiler (-> require("compiler"); ?cmpfun), see in the above *.Rmd
• Performance <-> Copying of R objects: "Traching memory" memory-copying.R script.
• Start looking at R packages, source and "binary"; at first packages and namespace: env-namespace.R

Week 7

• R packages, in source and "binary"; browsing Notes of "Package writing" course (Rnw and R files) (and the the "one" slide from week 2)
• package.skeleton()
• Packages and their Namespaces: Why are namespaces needed: Rmd whyNamespaces.Rmd and its html whyNamespaces.html.
• What happens when you call library(<pkg>) ?
• Understand more of How R Searches and Finds Stuff: Script week7-namespace-pkg.R

Extras

• a small script to get all methods of a generic function, nicely in a list, hidden or not.
• from lapply() to parLapply(): R's builtin package 'require(parallel)'

Lecture Attestation (Testat)

In order to obtain the ECTS credit you have to pass the exam -- answering some questions, and writing R code - in a *.Rmd (R Markdown file) at the end of the teaching block, specifically on April 15.

Recommended Reading

• Norman Matloff (2011) The Art of R Programming - A tour of statistical software design.
• Hadley Wickham (2013 ff) Advanced R
• Suraj Gupta (March 29, 2012) How R Searches and Finds Stuff

Miscellaneous on Programming (with R)

• "Literate Programming" by Donald Knuth
• "The Elements of Programming Style" by Kernighan and Plauger: Wikipedia,
• Quotes