The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously mentioned ProbABEL R packages. There are now a handful of useful R packages and other software utilities facilita... [Read more...]

Abhijit over at Stat Bandit posted some nice code for making forest plots using ggplot2 in R. You see these lots of times in meta-analyses, or as seen in the BioVU demonstration paper. The idea is simple - on the x-axis you have the odds ratio (or what... [Read more...]

In my previous post I showed you how to randomly split up a dataset into training and testing datasets. (Thanks to all those who emailed me or left comments letting me know that this could be done using other means. As things go with R, it's sometimes ... [Read more...]

Just saw the announcement of the availability of Rstudio, a new (free & open source) integrated development environment for R that works on Windows, Mac, and Linux. Judging from the screenshots, it looks like Rstudio supports syntax highlighting for Sweave & easy PDF creation from Sweave code, which is something I haven't ... [Read more...]

I recently analyzed some data trying to find a model that would explain body fat distribution as predicted by several blood biomarkers. I had more predictors than samples (p__n), and I didn't have a clue which variables, interactions, or quadratic terms made biological sense to put into a model. ... [Read more...]

When I have a question I usually ask the internet before bugging my neighbor. Yet it seems like Google's search results have become increasingly irrelevant over the last few years, and this is especially true for searching anything related to R (and pr... [Read more...]

Had a mental block today trying to figure out how to get the indices of columns in a data frame given their names. Simple task but difficult to search Google for an answer. Thanks to jashapiro, Matt, and Vince for giving me a heads up on the which() fu... [Read more...]

Something like this probably already exists in an R package somewhere out there, but I needed a function to summarize how much missing data I have in each variable of a data frame in R. Pass a data frame to this function and for each variable it'll give you the ... [Read more...]

I thought it would be trivial to extract the p-value on the F-test of a linear regression model (testing the null hypothesis R²=0). If I fit the linear model: fit [Read more...]

R evangelist David Smith, marketing VP at Revolution R, will be giving a webinar showing off some of the finer features of Revolution R Enterprise - an integrated development environment (IDE) for R that has an enhanced script editor with syntax highli... [Read more...]

I was recently reading a bit about logistic regression in a book on hierarchical/multilevel modeling when I first learned about the "divide by 4 rule" for quickly interpreting coefficients in a logistic regression model in terms of the predicted probabilities of the outcome. The idea is pretty simple. The logistic ... [Read more...]

A few months ago I showed you how to syntax-highlight R code using Github Gists for displaying R code on your blog or other online medium. The idea's really simple if you use blogger - head over to gist.github.com, paste in your R code, create a public "gist", ... [Read more...]

I recently reformatted my laptop and needed to reinstall R and all the packages that I regularly use. In a previous post I covered R Commander, a nice GUI for R that includes a decent data editor and menus for graphics and basic statistical analysis. Since Rcmdr depends on many ... [Read more...]

If you use blogger or even wordpress you've probably found that it's complicated to post code snippets with spacing preserved and syntax highlighting (especially for R code). I've discovered a few workarounds that involve hacking the blogger HTML templ... [Read more...]

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...]