Blog Archives

Write unit tests!

December 7, 2015
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Write unit tests!

Since 2000, I’ve been working on R/qtl, an R package for mapping the genetic loci (called quantitative trait loci, QTL) that contribute to variation in quantitative traits in experimental crosses. The Bioinformatics paper about it is my most cited; also see my 2014 JORS paper, “Fourteen years of R/qtl: Just barely sustainable.” It’s a bit

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Fitting linear mixed models for QTL mapping

November 24, 2015
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Fitting linear mixed models for QTL mapping

Linear mixed models (LMMs) have become widely used for dealing with population structure in human GWAS, and they’re becoming increasing important for QTL mapping in model organisms, particularly for the analysis of advanced intercross lines (AIL), which often exhibit variation in the relationships among individuals. In my efforts on R/qtl2, a reimplementation R/qtl to better

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Session info from R/Travis

September 25, 2015
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Session info from R/Travis

For the problem I reported yesterday, in which my R package was working fine locally but failing on Travis, the key solution is to run update.packages(ask=FALSE) locally, and maybe even update.packages(ask=FALSE, type="source") to be sure to grab the source of packages for which binaries are not yet available. I now know to do that. In

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It’s not you, it’s me

September 24, 2015
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It’s not you, it’s me

Somehow when my code stops working, my first (and second, and third) reaction is to blame everything except my own code. (“It’s not me, it’s you.”) And almost always, it’s my own code that’s the problem (hence the title of this post). I spent the day trying to resolve a bug in my early-in-development R

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Randomized Hobbit

June 22, 2015
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Randomized Hobbit

@wrathematics pointed me to his ngram R package for constructing and simulating from n-grams from text. I’d recently grabbed the text of the hobbit, and so I applied it to that text, with amusing results. Here’s the code I used to grab the text. Then calculate the ngrams with n=2. Simulate some number of words

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Initial steps towards reproducible research

December 4, 2014
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Initial steps towards reproducible research

In anticipation of next week’s Reproducible Science Hackathon at NESCent, I was thinking about Christie Bahlai’s post on “Baby steps for the open-curious.” Moving from Ye Olde Standard Computational Science Practice to a fully reproducible workflow seems a monumental task, but partially reproducible is better than not-at-all reproducible, and it’d be good to give people

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Error notifications from R

September 4, 2014
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Error notifications from R

I’m enthusiastic about having R notify me when my script is done. But among my early uses of this, my script threw an error, and I never got a text or pushbullet about that. And really, I’m even more interested in being notified about such errors than anything else. It’s relatively easy to get notified

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Notifications from R

September 3, 2014
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Notifications from R

You just sent a long R job running. How to know when it’s done? Have it notify you by beeping, sending you a text, or sending you a notification via pushbullet! beepr You can use Rasmus Bååth’s beepr package to have your computer play a sound. Install it from CRAN with Then, at the bottom

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Yet another R package primer

August 28, 2014
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Yet another R package primer

Hadley Wickham is writing what will surely be a great book about the basics of R packages. And Hilary Parker wrote a very influential post on how to write an R package. So it seems like that topic is well covered. Nevertheless, I’d been thinking for some time that I should write another minimal tutorial

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Testing an R package’s interactive graphs

August 1, 2014
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Testing an R package’s interactive graphs

I’ve been working on an R package, R/qtlcharts, with D3-based interactive graphs for quantitative trait locus mapping experiments. Testing the interactive charts it produces is a bit of a pain. It seems like I pretty much have to just open a series of examples in a web browser and tab through them manually, checking that

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