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 other packages, installing and loading Rcmdr like this... install.packages("Rcmdr", dependencies=TRUE)library(Rcmdr) ..
Blog Archives
Embed R Code with Syntax Highlighting on your Blog
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...
Writing my Thesis – Follow me on Twitter
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...
Deducer: R and ggplot2 GUI
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...
Quickly Find the Class of data.frame vectors in R
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...
Hadley Wickham’s ggplot2 / Data Visualization Course Materials
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...
QQ plot of p-values in R using base graphics
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...
All code on GGD is Free (Open Source BSD)
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.
Efficient Mixed-Model Association eXpedited (EMMAX) to Simutaneously Account for Relatedness and Stratification in Genome-Wide Association Studies
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 ...
Use SQL queries to manipulate data frames in R with sqldf package
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...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
