Blog Archives

Googling errors

February 14, 2014
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Googling errors

@roguelynn tweeted the other day: If attendees of this weekend’s intro to python workshop leave with one thing, it’ll be to Google your error messages first and foremost. I had just talked about the technique in my Tools for Reproducible Research course, and I had a few recent examples. Gtk-WARNING **: cannot open display: I […]

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knitr in a knutshell tutorial

February 7, 2014
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knitr in a knutshell tutorial

I spent a lot of time this week writing a short tutorial on knitr: knitr in a knutshell. This is my third little tutorial. (The previous ones were a git/github guide and a minimal make tutorial.) I’m pleased with these tutorials. In learning new computing skills, it can be hard to get started. My goal […]

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Code review

September 25, 2013
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Code review

There was an interesting news item in Nature on code review. It describes a project by some folks at Mozilla to review the code (well, really just 200-line snippets) from 6 selected papers in computational biology. There are very brief quotes from Titus Brown and Roger Peng. I expect that the author of the item, […]

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Department websites

September 12, 2013
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Department websites

I was thinking about department websites, partly because my own department’s website is terrible, and recently a colleague asked me whether I could suggest some good department sites. I’ll describe the basic principles for a good department website, and then I’ll comment on a number of examples. But first: No discussion of academic web pages […]

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“[” and “[[” with the apply() functions

August 20, 2013
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“[” and “[[” with the apply() functions

Did you know you can use "[" and "[[" as function names for subsetting with calls to the apply-type functions? For example, suppose you have a bunch of identifier strings like "ZYY-43S-CWA3" and you want to pull off the bit before the first hyphen ("ZYY" in this case). (For code to create random IDs like […]

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Electronic lab notebook

August 20, 2013
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Electronic lab notebook

I was interested to read C. Titus Brown‘s recent post, “Is version control an electronic lab notebook?” I think version control is really important, and I think all computational scientists should have something equivalent to a lab notebook. But I think of version control as serving needs orthogonal to those served by a lab notebook. […]

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Read the source code

August 6, 2013
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Read the source code

The other day, there was a bit of a twitter conversation about qqline in R. It made me think: how exactly is the line produced by qqline chosen? I seemed to recall that the line was through the first and third quartiles. An advantage of R is that you can just type the name of […]

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More on Chutes & Ladders

May 20, 2013
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More on Chutes & Ladders

Matt Maenner asked about the sawtooth pattern in the figure in my last post on Chutes & Ladders. Damn you, Matt! I thought I was done with this. Don’t feed my obsession. My response was that if the game ends early, it’s even more likely that it’ll be the kid who went first who won. […]

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Chutes & ladders: How long is this going to take?

May 17, 2013
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Chutes & ladders: How long is this going to take?

I was playing Chutes & Ladders with my four-year-old daughter yesterday, and I thought, “How long is this going to take?” I saw an interesting mathematical analysis of the game a few years ago, but it seems to be offline, though you can read it via the wayback machine. But that didn’t answer my specific […]

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Stack Exchange: Why I dropped out

May 13, 2013
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Stack Exchange: Why I dropped out

Stack Exchange is a series of question-and-answer sites, including Stack Overflow for programming and Cross Validated for statistics. I was introduced to these sites at a short talk by Barry Rowlingson at the 2011 UseR! meeting, “Why R-help must die!“ These sites have a lot of advantages over R-help: The format is easier to read, […]

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