Blog Archives

Quickly Find the Class of data.frame vectors in R

August 9, 2010
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Aviad Klein over at My ContRibution wrote a convenient R function to list the classes of all the vectors that make up a data.frame. You would think apply(kyphosis,2,class) would do the job but it doesn't - it calls every vector a character class. Aviad wrote an elegant little function that does the job perfectly without having to load any...

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Hadley Wickham’s ggplot2 / Data Visualization Course Materials

July 27, 2010
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Hadley Wickham, creator of ggplot2, an immensely popular framework for Tufte-friendly data visualization using R, is teaching two short courses at Vanderbilt this week. Once we opened registration to Vanderbilt students and staff we instantly filled al...

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QQ plot of p-values in R using base graphics

July 14, 2010
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Update Tuesday, September 14, 2010: Fixed the ylim issue, now it sets the y axis limit based on the smallest observed p-value. A while back Will showed you how to create QQ plots of p-values in Stata and in R using the now-deprecated sma package. A bi...

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All code on GGD is Free (Open Source BSD)

July 7, 2010
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At the request of a commenter I just wanted to clarify that any code released here for R or anything else is free and open source unless specifically stated otherwise. The open source BSD license for any code on GGD can be found on this copyright page.

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Efficient Mixed-Model Association eXpedited (EMMAX) to Simutaneously Account for Relatedness and Stratification in Genome-Wide Association Studies

June 9, 2010
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A few months ago I covered an algorithm called EMMA (Efficient Mixed-Model Association) implemented in R for simultaneously correct for both population stratification and relatedness in an association study. This method/software is very useful because ...

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Use SQL queries to manipulate data frames in R with sqldf package

May 25, 2010
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I've covered a few topics in the past including the plyr package, which is kind of like "GROUP BY" for R, and the merge function for merging datasets. I only recently found the sqldf package for R, and it's already one of the most useful packages I've ever installed. The main function in the package is sqldf(), which takes...

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Tutorial: Principal Components Analysis (PCA) in R

May 20, 2010
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Found this tutorial by Emily Mankin on how to do principal components analysis (PCA) using R. Has a nice example with R code and several good references. The example starts by doing the PCA manually, then uses R's built in prcomp() function to do the s...

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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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