Tutorial- Building Biological Networks

April 4, 2013
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Tutorial- Building Biological Networks

I love networks! Nothing is better for visualizing complex multivariate relationships be it social, virtual or biological. I recently gave a hands-on network building tutorial using R and Cytoscape to build large biological networks. In these networks Nodes represent metabolites and edges can be many things, but I specifically focused on biochemical relationships and chemical

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Demographic analysis using the `popbio` library and some other fun stuff

April 4, 2013
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Demographic analysis using the `popbio` library and some other fun stuff

This week at the Davis R Users’ Group we had a great presentation by Kara Moore O’Leary on using the popbio package to examine rare plant demographics. The following is her script run through knitr. You can download the original script and associated data here. Find out more about Kara and her work at...

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R 3.0 released; ggplot2 stat_summary bug fixed!

April 4, 2013
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The new version of R was released yesterday. As I understand it, the numbering change to 3.0 represents the recognition that R had evolved enough to justify a new number rather than the addition of many new features. There are some important new featur...

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An Introduction to SAS for R Programmers

April 4, 2013
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by Joseph Rickert Life decisions are usually much too complicated to be attributed to any single cause, but one important reason that I am here at Revolution today is that I ignored suggestions from well-meaning faculty back in graduate school to work more in SAS rather than doing everything in R. There was a heavy emphasis on SAS then:...

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List of Bioinformatics Workshops and Training Resources

April 4, 2013
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I frequently get asked to recommend workshops or online learning resources for bioinformatics, genomics, statistics, and programming. I compiled a list of both online learning resources and in-person workshops (preferentially highlighting those where workshop materials are freely available online):List of Bioinformatics Workshops and Training ResourcesI hope to keep the page above as up-to-date as possible....

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Test from knitr to wordpress

April 4, 2013
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Test from knitr to wordpress

Title This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages (click the MD toolbar button for help on Markdown). When you click the Knit HTML button a web page will be generated that includes both content as well as the output of any embedded R code chunks within

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Measuring the Intensity of Historical Crises with VaR (Part 2)

April 4, 2013
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Measuring the Intensity of Historical Crises with VaR (Part 2)

Adam Duncan, December 2012Also avilable on R-bloggers.com If you missed the first part of this analysis, be sure to check it out on gtog.github.com.In this part of the analyis, I’m going to look at the actual 1 day negative returns / VaR estimates (“VaR breaks”) across a numnber of different asset classes. The hope is to arrive at...

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Construct an unique index from two integer (Pairing Function)

April 3, 2013
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Construct an unique index from two integer (Pairing Function)

Recently, I need to construct an unique index from two integer. The best solution I found is the Pairing function. Pairing function is an one to one and onto function that map two integers to a single integer. The definition as follows: If ordering of x and y is not important, we can swap x

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Interactive visualization of survival curves with Shiny

April 3, 2013
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Interactive visualization of survival curves with Shiny

We have a growing interest in using our favorite tools (R and Mathematica) to build web interfaces to interactively explore and visualize data. Our last 5 posts have involved interactive tools, namely Mathematica’s computable document format and R’s new Shiny package. There is a new kid on the block for interactive visualization tools in R,

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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
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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 … 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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R 3.0.0 is released!

April 3, 2013
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R 3.0.0 is released!

The new R 3.0.0 is out! You know the drill! Get the source code from here.

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Colour it up: my quest to master ggplot2 (part 2)

April 3, 2013
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Splitting a Large CSV File into Separate Smaller Files Based on Values Within a Specific Column

April 3, 2013
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Splitting a Large CSV File into Separate Smaller Files Based on Values Within a Specific Column

One of the problems with working with data files containing tens of thousands (or more) rows is that they can become unwieldy, if not impossible, to use with “everyday” desktop tools. When I was Revisiting MPs’ Expenses, the expenses data I downloaded from IPSA (the Independent Parliamentary Standards Authority) came in one large CSV file

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

April 3, 2013
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CFP: the 11th Australasian Data Mining Conference (AusDM 2013), submission due 15 July

********************************************************************* 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 →

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Beware of grep with a list

April 2, 2013
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Beware of grep with a list

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 that starts with "c(", grep finds

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apply vs for

April 2, 2013
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apply vs for

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 iteration being retained in memory. Here’s a

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x[[c(5,3)]]

April 2, 2013
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x[[c(5,3)]]

An R tip: Did you know that x] is the same as x]]? I should make more thorough use of this. In the help file for ] is equivalent to alist]...] providing all but

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Personal R Packages

April 2, 2013
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Personal R Packages

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 →

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2013-3 Generating unique names in gridSVG

April 2, 2013
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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 →

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Revisiting MPs’ Expenses

April 2, 2013
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Revisiting MPs’ Expenses

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 (a bellweather of the extent of

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