A few weeks ago I suddenly reached the point that every graduate student once thought would never come - time to start writing my thesis. With a blank page and a blinking cursor staring me in the face it's time to compile all of my published and unpubl... [Read more...]

Last Year I introduced you to R Commander, a nice graphical user interface (GUI) for R for those of you who are still hesitant to leave the clicky-box style research a la SPSS for the far more superior reproducible research using R. As most of you know... [Read more...]

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 ... [Read more...]

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... [Read more...]

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... [Read more...]

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. [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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... [Read more...]

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... [Read more...]

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 ... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

In a previous tutorial I showed you how to create plots faceted by the level of a third variable using ggplot2. A commenter asked about using faceted plots and viewports and reminded me of this function I found in the ggplot2 Google group. The arrange function below is similar to ... [Read more...]