Blog Archives

My JSM 2016 itinerary

July 27, 2016
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My JSM 2016 itinerary

The Joint Statistical Meetings are in Chicago next week. I thought I’d write down the set of sessions that I plan to attend. Please let me know if you have further suggestions. First things first: snacks. Search the program for “spotlight” or “while supplies last” for the free snacks being offered. Or go to the […]

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I am a data scientist

April 8, 2016
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I am a data scientist

Three years ago this week, I wrote a blog post, “Data science is statistics”. I was fiercely against the term at that time, as I felt that we already had a data science, and it was called Statistics. It was a short post, so I might as well quote the whole thing: When physicists do […]

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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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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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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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Reproducibility is hard

September 9, 2015
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Reproducibility is hard

Reproducibility is hard. It will probably always be hard, because it’s hard keeping things organized. I recently had a paper accepted at G3, concerning a huge set of sample mix-ups in a large eQTL study. I’d discovered and worked out the issue back in December, 2010. I gave a talk about it at the Mouse […]

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Reproducibility is hard

September 9, 2015
By
Reproducibility is hard

Reproducibility is hard. It will probably always be hard, because it’s hard keeping things organized. I recently had a paper accepted at G3, concerning a huge set of sample mix-ups in a large eQTL study. I’d discovered and worked out the issue back in December, 2010. I gave a talk about it at the Mouse […]

Read more »


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