Monthly Archives: April 2013

A brief note: R 3.0.0 and bioinformatics

April 3, 2013
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A brief note: R 3.0.0 and bioinformatics

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 simpleaffy package from Bioconductor

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R version 3 released

April 3, 2013
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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 makes sense. Nonetheless, this release does include some...

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Tables Are Like Cockroaches

April 3, 2013
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Tables Are Like Cockroaches

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 paper concludes with As part of...

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Quickly Profiling Compiled Code within R on the Mac

April 3, 2013
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Quickly Profiling Compiled Code within R on the Mac

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 the methods are platform dependent, with linux requiring command line tools

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R 3.0.0 is released! (what’s new, and how to upgrade)

April 3, 2013
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R 3.0.0 is released! (what’s new, and how to upgrade)

A few hours ago Peter Dalgaard (of R Core Team) announced the release of R 3.0.0!  Bellow you can read the changes in this release. One of the features worth noticing is the introduction of long vectors to R 3.0.0. As David Smith …Read more »

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Managing memory in a list of lists data structure

April 3, 2013
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First, a confession: instead of using classes and defining methods for them, I build a lot of ad hoc data structures out of lists and then build up one-off methods that operate on those lists of lists. I think this is a perl-ism that has transferred into my R code. I might eventually learn how

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Managing memory in a list of lists data structure

April 3, 2013
By

First, a confession: instead of using classes and defining methods for them, I build a lot of ad hoc data structures out of lists and then build up one-off methods that operate on those lists of lists. I think this … Continue reading →

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ISBA on INLA [webinar]

April 3, 2013
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ISBA on INLA [webinar]

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 to https://www.webex.com/login/attend-a-meeting

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Automated Re-Install of Packages for R 3.0

April 3, 2013
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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 default install to the Library: Automated Re-Install of...

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Hurray! An R Connections API!

April 3, 2013
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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. Until now, the only

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