Monthly Archives: January 2010

A new twist on the identifier mapping problem

January 11, 2010
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A new twist on the identifier mapping problem

Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, but that’s apparently way too

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Typos in Chapter 5

January 11, 2010
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Typos in Chapter 5

After writing the solutions to the odd-numbered exercises in Chapter 5 of “Introducing Monte Carlo Methods with R”., I alas found the following typos, two of which are rather major (Exercise 5.3 and Example 5.16). I apologise to the readers these typos may confuse. – Exercise 5.3 has no simple encompassing set and the constraint should

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R exams

January 11, 2010
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R exams

As posted yesterday, today was the day of my Exploratory Statistics exam, turned into 3 R exams because of the lack of terminals for the students to work on. (We tried to encourage students to use their own laptop but less than twenty registered…) If you happen to be interested in those exams, they are

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Bay Area User Group: R-Powered Web Apps

January 11, 2010
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For those in the San Francisco area, tomorrow night's Bay Area R User Group meeting -- to be held at Twitter's HQ -- is a must-see. The theme is "R-Powered Web Apps" and features guest speakers Jeroen Ooms and Jeff Horner. (Disclosure: REvolution Computing is sponsoring Jeroen's appearance at this event.) We've featured Jeroen's awesome web-based applications using R...

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ggplot2 Tutorial: Scatterplots in a Series of Small Multiples

January 11, 2010
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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...

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Lattice: Multivariate Data Visualization with R

January 11, 2010
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Lattice: Multivariate Data Visualization with R

I have just reviewed Sarkar‘s Lattice: Multivariate Data Visualization with R for the Journal of the Royal Statistical Society Series A.  I would highly recommend the book to all R users who wish to produce publication quality g...

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RClimate Script Introduction

January 10, 2010
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RClimate Script Introduction

Would you like to be able to generate a GISS temperature anomaly trend chart on your PC with just 1 line of R script? What about downloading the R script to your PC so that you can edit the script to fit your needs?In this post I present my first RClimate Script so that users

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Progress bars in R (part II) – a wrapper for apply functions

January 10, 2010
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Progress bars in R (part II) – a wrapper for apply functions

In a previous post I gave some examples of how to make a progress bar in R. In the examples the bars were created within loops. Very often though I have situations where I would like have a progress bar when using apply(). The plyr package provides several apply-like functions also including progress bars, so

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LSPM with snow

January 10, 2010
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LSPM with snow

My last post provided examples of how to use the LSPM package. Those who experimented with the code have probably found that constrained optimizations with horizons > 6 have long run-times (when calc.max >= horizon).This post will illustrate how the s...

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Outlawing Gay Marriage

January 10, 2010
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Given the recent votes on same-sex marriage in New Jersey and Portugal, I wanted to test a seemingly innocuous claim that touches upon very broad issues in political theory: does the degree of directness of a “democratic” vote predict whether the vote will promote or prohibit same-sex marriage? Naively, it seemed clear to me that

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