Publications by Karl Broman
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. As Tit...
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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 that, see the end of this post.) Suppose ...
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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 was to provide the initial motivation and ...
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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 was logged into a...
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“[” with the apply() functions, revisited
I’d mentioned in the fall that one could use "[" in the apply-type functions, like this: id <- c("ZYY-43S-CWA3", "6YU-F4B-VD2I") sapply(strsplit(id, "-"), "[", 2) I just realized that you can use this with matrices, too. If you have a list of matrices, you can pull out rows and columns with this technique. z <- list(matrix(1:10, nrow=2), matri...
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Crayon colors in R
Last night I was working on a talk on creating effective graphs. Mostly, I needed to update the colors, as there’d been some gaudy ones in its previous form (e.g., slide 22). I usually pick colors using the crayons in the Mac Color Picker. But that has just 40 crayons, and I wanted more choices. That led me to the list of Crayola crayon colors ...
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Two more points about crayon colors
If you want to use crayon colors in R but you don’t want to rely on my R/broman package, you can just grab the code. Copy the relevant lines from the R/brocolors.R file: crayons = c("Almond"="#efdecd", "Antique Brass"="#cd9575", "Apricot"="#fdd9b5", ... "Yellow Green"="#c5e384", "Yello...
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Further points on crayon colors
I saw this great post on crayola crayon colors at the Learning R blog, reproducing a nice graph of the Crayola crayon colors over time. (Also see this even nicer version.) The Learning R post shows how to grab the crayon colors from the wikipedia page, “List of Crayola crayon colors,” directly in R. Here’s the code (after some slight modifi...
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hipsteR: re-educating people who learned R before it was cool
This morning, I started a tutorial for folks whose knowledge of R is (like mine) stuck in 2001. Yesterday I started reading the Rcpp book, and on page 4 there’s an example using the R function replicate, which (a) I’d never heard before, and (b) is super useful. I mean, I often write code like this, for a bootstrap: x <- rnorm(2500) sapply(1:...
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2014 UseR conference, days 1-2
I’m at UCLA for the UseR Conference. I attended once before, and I really enjoyed it. And I’m really enjoying this one. I’m learning a ton, and I find the talks very inspiring. In my comments below, I give short shrift to some speakers (largely by not having attended their talks), and I’m critical in some places about the conference org...
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