Blog Archives

An enhanced Kaplan-Meier plot

March 8, 2011
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An enhanced Kaplan-Meier plot

We often see, in publications, a Kaplan-Meier survival plot, with a table of the number of subjects at risk at different time points aligned below the figure. I needed this type of plot (or really, matrices of such plots) for an upcoming publication. Of course, my preferred toolbox was R and the ggplot2 package. There

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RStudio: a cut above

March 1, 2011
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RStudio: a cut above

As most followers of R-bloggers.com and the Twitter #rstats know by now, RStudio is a new open-source IDE for R that was beta-released yesterday. I have started putting it through its paces within my R workflow, and my impressions are more than favorable. I also tried it out on my home Linux server in server

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The split-apply-combine paradigm in R

February 25, 2011
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The split-apply-combine paradigm in R

Last night at the DC R Users meetup, which was our largest meetup to date, I gave an introductory presentation on data munging, and spent a bit of time on the split-apply-combine paradigm that I use almost daily in my work. I talked mainly about the packages plyr and doBy, which I use a lot

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ggplot2 joy

February 25, 2011
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ggplot2 joy

I’ve been working on a long-term (25+yr) longitudinal study of rheumatoid arthritis with my boss. He just walked in and asked if I could create a plot showing the trajectory of pain scores over time for each subject, separated by educational level (4 groups). Having now worked with ggplot2 for a while, and learning more

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Forest plots using R and ggplot2

October 31, 2010
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Forest plots using R and ggplot2

Forest plots are most commonly used in reporting meta-analyses, but can be profitably used to summarise the results of a fitted model. They essentially display the estimates for model parameters and their corresponding confidence intervals. Matt Shotwell just posted a message to the R-help mailing list with his lattice-based solution to the problem of creating forest plots in R. I

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useR! 2010 done and dusted

July 23, 2010
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useR! 2010 done and dusted

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A small customization of ESS

May 14, 2010
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A small customization of ESS

JD Long (at Cerebral Mastication) posted a question on Twitter about an artifact in ESS, where typing “_” gets you “<-”. This is because in the early days of S+, “_” was an allowed assignment operator, and ESS was developed in that era. Later, it was disallowed in favor of “<-” and “=”, so ESS

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Quick and dirty parallel processing in R

April 30, 2010
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Quick and dirty parallel processing in R

R has some powerful tools for parallel processing, which I discovered while searching for ways to fully utilize my 8-core computer at work. What surprised me is how easy it is…about 6 lines of code, if that. Given that I wasn’t allowed to install heavy duty parallel-processing systems like MPICH on the computer, I found

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R amusements

March 5, 2010
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R amusements

On a lark, and to kill a bit of time, I was running the R fortune command looking for references to SAS. Here’s what two successive random fortunes turned up. Can there be two more antipodal opinions about the same product? I laughed out loud. > fortune(‘SAS’) There are companies whose yearly license fees to

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Workflow with Python and R

March 6, 2009
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Workflow with Python and R

I seem to be doing more and more with Python for work over and above using it as a generic scripting language. R has been my workhorse for analysis for a long time (15+ years in various incarnations of S+ and R), but it still has some deficiencies. I’m finding Python easier and faster to

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