Blog Archives

Analysis of ISMB coverage at FriendFeed: 2008 – 2011

July 27, 2011
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Analysis of ISMB coverage at FriendFeed: 2008 – 2011

ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting. Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB at FriendFeed now

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R: calculations involving months

July 7, 2011
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R: calculations involving months

Ask anyone how much time has elapsed since September last year and they’ll probably start counting on their fingers: “October, November…” and tell you “just over 9 months.” So, when faced as I was today with a data frame (named dates) like this: How to add a 7th column, with the number of months between

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Syntax highlighting of R code at WordPress.com

May 20, 2011
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Syntax highlighting of R code at WordPress.com

If your WordPress blog is hosted at WordPress.com (like this one), you may know that source code in posts is formatted and highlighted using a shortcode, as explained here. Until recently, R was not on the list of supported languages (neither was Perl), but I noticed today that both of them are now supported. This

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Friday fun with: Google Trends

May 19, 2011
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Friday fun with: Google Trends

Some years ago, Google discovered that when people are concerned about influenza, they search for flu-related information and that to some extent, search traffic is an indicator of flu activity. Google Flu Trends was born. Illness is sweeping through our department this week and I have succumbed. It’s not flu but at one point, I

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Friday fun projects

May 14, 2011
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Friday fun projects

What’s a “Friday fun project”? It’s a small computing project, perfect for a Friday afternoon, which serves the dual purpose of (1) keeping your programming/data analysis skills sharp and (2) providing a mental break from the grind of your day job. Ideally, the skills learned on the project are useful and transferable to your work

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R 2.12 to 2.13 package upgrade

April 14, 2011
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R 2.12 to 2.13 package upgrade

If you: use Linux have just upgraded your R installation from 2.12 to 2.13 installed some/all of your packages in your home area (e.g. ~/R/i486-pc-linux-gnu-library/2.12) and… …are wondering why R can’t see them any more just do this: # at a shell prompt cp ~/R/i486-pc-linux-gnu-library/2.12 ~/R/i486-pc-linux-gnu-library/2.13 # in R console update.packages(checkBuilt=TRUE, ask=FALSE) # back to

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Fixing aberrant files using R and the shell: a case study

April 7, 2011
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Fixing aberrant files using R and the shell: a case study

Once in a while, you embark on what looks like a simple computational procedure only to encounter frustration very early on. “I can’t even read my file into R!” you cry. Step back, take a deep breath and take note of what the software is trying to tell you. Most times, you’ve just missed something

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The RStudio IDE: first impressions are positive

February 28, 2011
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The RStudio IDE: first impressions are positive

Integrated development environments (IDEs) are software development tools, providing an interface that enables you to write, debug, run and view the output of your code. Whether you need an IDE or find them useful depends very much on your own preferences and style of working. In my own case for example, I’ve tried both Eclipse

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Analysis of retractions in PubMed

November 30, 2010
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Analysis of retractions in PubMed

As so often happens these days, a brief post at FriendFeed got me thinking about data analysis. Entitled “So how many retractions are there every year, anyway?”, the post links to this article at Retraction Watch. It discusses ways to estimate the number of retractions and in particular, a recent article in the Journal of

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Findings increasingly novel, scientists say…

October 29, 2010
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Findings increasingly novel, scientists say…

…was the tongue-in-cheek title of an image that I posted to Twitpic this week. It shows the usage of the word “novel” in PubMed article titles over time. As someone correctly pointed out at FriendFeed, it needs to be corrected for total publications per year. It was inspired by a couple of items that caught

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