Monthly Archives: January 2010

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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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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RClimate Script: CO2 Trends

January 20, 2010
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RClimate Script: CO2 Trends

This RClimate Script lets users retrieve the latest data file on monthly Mauna Loa  CO2 levels and generate a trend chart with the latest reading highlighted. CO2 Trends – Keeling Curve Here’s the Mauna Loa Observatory CO2 trend from 1958 to Dec., 2009. Here are the data and RClimate Script links: Data Link RClimate Script link Posted in

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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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Introduce your friends to R

January 19, 2010
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R has gotten quite a lot of exposure recently. It started with the feature article in the New York Times last January, but since then there's been a steady flow of articles about R in analyst reports, on blogs, in YouTube videos, on Twitter, as well as in the general news media. As a result, a lot of new...

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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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