Publications by Stephen Turner
Seminar: Reproducible Research with R, LaTeX, & Sweave
Theresa Scott, instructor of the previously mentioned R workshop and weekly R clinic, is giving a lecture entitled “Reproducible Research with R, LaTeX, & Sweave” in MRB III, room 1220, this Wednesday 11/18 at 1:30. You can see more details about the lecture here. Looks like her slides as well as much more introductory material...
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NYT: SAS threatened by R
The New York Times had an interesting piece yesterday about how SAS is facing several business threats from companies like the recently IBM-acquired SPSS, and from burgeoning interest in open-source software like R. The NYT ran an entire article about R earlier this year, and this article discusses how SAS has been revamping their t...
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Get Started with Machine Learning in R
A Beautiful WWW put together a great set of resources for getting started with machine learning in R. First, they recommend the previously mentioned free book, The Elements of Statistical Learning. Then there’s a link to a list of dozens of machine learning and statistical learning packages for R. Next, you’ll need data. H...
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Browse R Graphics with the R Graph Gallery and the R Graphical Manual
One of R’s biggest strengths is its unparalleled graphing capabilities. Just see any of our previous posts on ggplot2, visualization, or other posts tagged with R. R has several fundamentally different systems for plotting, including base graphics, lattice, and ggplot2. Furthermore, many add-on packages come with their own funct...
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Capture system commands as R objects with system(…, intern=T)
Just discovered this very handy R command to capture the output from a system command as an R object. I wanted to use R to read in the output from another program (PLINK) and do some processing on each output file. Of course if the files are named sequentially (plink1.out, plink2.out, plink3.out, etc.) this would be simple with a fo...
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Use plyr instead of _apply() in R
I’ve covered plyr once before, showing you how to get means and variances for two quantitative traits across multilocus genotypes. JD Long over at Cerebral Mastication recently posted a nice screencast illustrating how plyr “just works” as an alternative to R’s family of apply commands. There’s a set of R functions (apply,...
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New Features in ggplot2 0.8.5
Learning R blog details some of the new features in the latest update to ggplot2. The latest version includes functions to make it easier to change axis and legend labels, as well as a function to easily set the limits of the plot display outside the range of the data. Be sure to check back next week – I’m putting together a shor...
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ggplot2 Tutorial: Scatterplots in a Series of Small Multiples
It took several months after learning about ggplot2 before I gave it a try myself. I was apprehensive about learning a new graphics system with a new set of commands. Thing is, if you’ve ever used plot() in R, you already know how to use much of the functionality in ggplot2! In this tutorial I want to show you just how easy it...
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Coming to R from SQL, Python, SAS, Matlab, or Lisp
Head over to Revolutions Blog for a list of PDF and powerpoint resources for making the transition to R from other programming or stats languages. All of these notes come from the New York R meetup. I enjoyed browsing the meetup’s files – lots of powerpoints, PDFs, and example R data files for various topics, including several s...
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GWAS Manhattan plots and QQ plots using ggplot2 in R
Will posted earlier this week about how to produce manhattan plots of GWAS results using Stata, so I thought I’d share how I do this in R using ggplot2. First, if you’ve never used ggplot2, you’ll need to add it to your R installation by typing: install.packages(“ggplot2”) Once you’ve done that, copy and paste this comm...
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