April 2013

A brief note: R 3.0.0 and bioinformatics

April 3, 2013 | nsaunders

Today marks the release of R 3.0.0. There will be plenty of commentary and useful information at sites such as R-bloggers (for example, Tal’s post). Version 3.0.0 is great news for bioinformaticians, due to the introduction of long vectors. What does that mean? Well, several months ago, I was using the ... [Read more...]

R version 3 released

April 3, 2013 | David Smith

The R language marks a major milestone today with the release of R 3.0.0 (codename: "Masked Marvel"). The increment in the version number reflects not a fundamental change in the R langauge itself, but a recognition that the R codebase has matured to a point where closing out the 2.x series ... [Read more...]

Tables Are Like Cockroaches

April 3, 2013 | klr

As much as I would like to completely replace all tables with beautiful, intuitive, and interactive charts, tables like cockroaches cannot be eliminated. Based on this very interesting discussion on the Perceptual Edge forum with source Exploring the Origins of Tables for Information Visualization, tables date back to 1850 BCE. The ...
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Quickly Profiling Compiled Code within R on the Mac

April 3, 2013 | Ian

This is a quick note on profiling your compiled code on the mac. It is important not to guess when figuring out where the bottlenecks in your code are, and for this reason, the R manual has several suggestions on how to profile compiled code running within R. All of ... [Read more...]

ISBA on INLA [webinar]

April 3, 2013 | xi'an

If you have missed the item of information, Håvard Rue is giving an ISBA webinar tomorrow on INLA: the ISBA Webinar on INLA is scheduled for April 4th, 2013 from 8:30 - 12:30 EDT. ------------------------------------------------------- To join the online meeting (Now from mobile devices using the Cisco WebEx Meeting App) ------------------------------------------------------- 1. Go ... [Read more...]

Automated Re-Install of Packages for R 3.0

April 3, 2013 | Randy Zwitch

With the big release of R 3.0 today comes an unfortunate side effect of needing to re-install all of your packages. Luckily, R provides a pretty easy method of getting all of your packages into a list for automated re-install.  Here’s how to do it for OSX users with a ... [Read more...]

Hurray! An R Connections API!

April 3, 2013 | BioStatMatt

I waited until April 3 to post this, so it wouldn't be taken as an April Fool's joke! A recent R News item announces that we now have a bona fide mechanism to create custom connections in R! This makes it possible to implement a custom connection in an R package. ... [Read more...]

CFP: the 11th Australasian Data Mining Conference (AusDM 2013), submission due 15 July

April 3, 2013 | Yanchang Zhao

********************************************************************* The 11th Australasian Data Mining Conference (AusDM 2013) Canberra, Australia, 13-15 November 2013, http://ausdm13.togaware.com Join us on LinkedIn: http://www.linkedin.com/groups/AusDM-4907891 ********************************************************************* Data mining, the art and science of intelligent analysis of (usually large) data sets for meaningful (and previously unknown) … Continue reading → [Read more...]

Beware of grep with a list

April 2, 2013 | Karl Broman

Another R tip: beware of as.character applied to a list. Really, beware of grep with a list: You might have thought that the result would be just 1, but grep expects a vector of character strings. If the input is not that, it uses as.character(). Since the result of ... [Read more...]

apply vs for

April 2, 2013 | Karl Broman

It’s widely understood that, in R programming, one should avoid for loops and always try to use apply-type functions. But this isn’t entirely true. It may have been true for Splus, back in the day: As I recall, that had to do with the entire environment from each ... [Read more...]

x[[c(5,3)]]

April 2, 2013 | Karl Broman

An R tip: Did you know that x[[c(5,3)]] is the same as x[[5]][[3]]? I should make more thorough use of this. In the help file for [[: [[ can be applied recursively to lists, so that if the single index i is a vector of length p, alist[[i]] is equivalent ... [Read more...]

Personal R Packages

April 2, 2013 | hilaryparker

I came across this R package on GitHub, and it made me so excited that I decided to write a post about it. It’s a compilation by Karl Broman of various R functions that he’s found helpful to write throughout … Continue reading → [Read more...]

2013-3 Generating unique names in gridSVG

April 2, 2013 | akoh003

The gridSVG package exports grid images to the SVG image format for viewing on the web. This article describes the problems associated with retaining grid object names in SVG element id attributes. In addition, new features in gridSVG that allow … Continue reading → [Read more...]

Revisiting MPs’ Expenses

April 2, 2013 | Tony Hirst

I couldn’t but notice the chatter about Iain Duncan Smith claiming he’d have no problem “living on 53 pounds a dayweek“, which made me wonder not only how many meal catered events he attends each week (and how many of his scheduled meeting also have complementary tea and biscuits (... [Read more...]

a brief on naked statistics

April 2, 2013 | xi'an

Over the last Sunday breakfast I went through Naked Statistics: Stripping the Dread from the Data. The first two pages managed to put me in a prejudiced mood for the rest of the book. To wit: the author starts with some math bashing (like, no one ever bothers to tell ... [Read more...]
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