Monthly Archives: January 2010

ggplot2: Crayola Crayon Colours

January 21, 2010
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ggplot2: Crayola Crayon Colours

Statistical Algorithms blog attempted to recreate a graph depicting the growing colour selection of Crayola crayons in ggplot2 (original graph below via FlowingData). He also asked the following questions: Is there an easier way to do this? How can I make the axes more like the original? What about the white lines between boxes and

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Scheduled Parallel Computing with R: R + Rmpi + OpenMPI + Sun Grid Engine (SGE)

January 20, 2010
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Recently I’ve learned how to do parallel computing in R on a cluster of machines thanks to the R packages snowfall, snow, and Rmpi. I’ve been using the SOCKET method with snowfall since together they make things simple. With these tools, I can reduce day/week long jobs to hours or a day across many (100)

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Remote download and viewing of brain atlas

January 20, 2010
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Remote download and viewing of brain atlas

The dcemriS4 package allows one to easily import and display NIfTI-1 class data sets. The following code takes the MNI152 brain atlas from the WWW and produces an orthographic display using the mid-axial, mid-sagittal and mid-coronal planes.

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How to integrate R into web-based applications (video)

January 20, 2010
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The slides and videos from Jeff Horner's talk at last week's Bay Area User Group session on R-Powered Web Apps are now available. I've embedded it here below, but you might want to click through to larger size for better readability on the slides. Jeff's talk (titled "Use Rapache! It works") gives an overview of how to integrate R...

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GWAS Manhattan plots and QQ plots using ggplot2 in R

January 20, 2010
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Will posted earlier this week about how to produce manhattan plots of GWAS results using Stata, so I thought I'd share how I do this in R using ggplot2. First, if you've never used ggplot2, you'll need to add it to your R installation by typing: install.packages("ggplot2") Once you've done that, copy and paste this command to download the functions I wrote...

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Example 7.23: the Monty Hall problem

January 20, 2010
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Example 7.23: the Monty Hall problem

The Monty Hall problem illustrates a simple setting where intuition often leads to a solution different from formal reasoning. The situation is based on the game show Let's Make a Deal. First, Monty puts a prize behind one of three doors. Then the player chooses a door. Next, (without moving the pize) Monty opens an...

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New UseR group in Seattle, WA

January 19, 2010
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There's a new local R user group to add to the list. The latest addition is in Seattle, WA and the first meeting of the Seattle useR Group is tomorrow. The group is organized by Zack Stednick (a data analyst and R user at the Fred Hutchinson Cancer Research Center in Seattle), and this meeting is hosted by my...

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Solution manual for Introducing Monte Carlo Methods with R

January 19, 2010
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Solution manual for Introducing Monte Carlo Methods with R

After the complete solution manual for Bayesian Core, the solution manual for the odd numbered exercises of “Introducing Monte Carlo Methods with R” is now arXived. The fuller 133 page version for instructors is available from Springer Verlag by demand only, in order to keep the appeal of the book as a textbook (even

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New features in ggplot2 version 0.85

January 18, 2010
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Hadley Wickham recently updated the ggplot2 package for R to version 0.8.5. In addition to bugfixes and performance improvements, this version introduces some handy new features. Among them: the ability to display mathematical equations as text, automatic legends for color scales, and user-configurable axis labels and legend titles. The Learning R blog runs through the new features with worked...

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Coming to R from SQL, Python, SAS, Matlab, or Lisp

January 18, 2010
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Head over to Revolutions Blog for a list of PDF and powerpoint resources for making the transition to R from other programming or stats languages.  All of these notes come from the New York R meetup. I enjoyed browsing the meetup's files - lots of powerpoints, PDFs, and example R data files for various topics, including several slideshows on...

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