Blog Archives

Using R, LaTeX, and Sweave for Reproducible Research: Handouts, Templates, & Other Resources

May 13, 2010
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Several readers emailed me or left a comment on my previous announcement of Frank Harrell's workshop on using Sweave for reproducible research asking if we could record the seminar. Unfortunately we couldn't record audio or video, but take a look a...

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Sweave for Reproducible Research and Beatiful Statistical Reports

May 11, 2010
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Frank Harrell, chair of the Biostatistics department here at Vanderbilt, is giving a seminar entitled "Sweave for Reproducible Research and Beautiful Statistical Reports" tomorrow, Wednesday, May 12, 1:30-2:30pm, in the MRBIII Conference Room 1220. This tutorial covers the basics of Sweave and shows how to enhance the default output in various ways by using: latex methods for converting R...

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R Package ‘rms’ for Regression Modeling

May 11, 2010
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If you attended Frank Harrell's Regression Modeling Strategies course a few weeks ago, you got a chance to see the rms package for R in action. Frank's rms package does regression modeling, testing, estimation, validation, graphics, prediction, and ty...

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Mixed linear model approach adapted for genome-wide association studies

May 6, 2010
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A few weeks ago I covered an R package for efficient mixed model regression that is capable of simultaneously accounting for both population stratification and relatedness to compute unbiased estimates of standard errors and p-values for genetic associ...

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Top 10 Algorithms in Data Mining

April 23, 2010
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The authors here invited ACM KDD Innovation Award and IEEE ICDM Research Contributions Award winners to each nominate up to 10 best-known algorithms in data mining, including the algorithm name, justification for nomination, and a representative public...

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Efficient Mixed-Model Association in GWAS using R

April 13, 2010
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I recently did an analysis for the eMERGE network where I had lots of individuals from a small town in central Wisconsin where many of the subjects were related to one another. The subjects could not be treated as independent, but I could not use a fam...

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ProbABEL – R package for GWAS data imputation

April 6, 2010
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I've been using GenABEL for some time now for GWAS analysis using related individuals. It has an excellent set of functions for estimating a kinship matrix from a dense marker panel and then using this in a linear mixed effects model to allow for relat...

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Frank Harrell’s Regression Modeling Strategies Course Handouts

April 1, 2010
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The previously mentioned Regression Modeling Strategies short course taught by Frank Harrell is nearly over. Here are the handouts (PDF) from the course. Keep an eye out here, I'll be writing a few more posts in the near future on topics Frank covered...

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Video: ggplot2 Creator Hadley Wickham’s Short Course on Data Visualization Using R

March 23, 2010
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Hadley Wickham, creator of ggplot2, has posted a 2 hour video on data visualization using R. You can find links to the videos and slides over at Revolutions Blog. Check back here soon. I am working with Hadley to arrange a day-long ggplot2 short cours...

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Create annotated GWAS manhattan plots using ggplot2 in R

March 18, 2010
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A few months ago I showed you in this post how to use some code I wrote to produce manhattan plots in R using ggplot2. The qqman() function I described in the previous post actually calls another function, manhattan(), which has a few options you can s...

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