## The avalanche of publications mentioning GO

November 30, 2010
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Gene Ontology is the de facto standard for annotation of gene products. It has been widely used in biological data mining, and I believe it will play more central role in the future. Publications mentioning GO was collected and deposited in GO ftp, and can be accessed (ftp://ftp.geneontology.org/go/doc/). Read More: 454 Words Totally

## RQuantLib 0.3.5

November 30, 2010
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The new RQuantLib release 0.3.5 is now on CRAN and in Debian. RQuantLib combines (some of) the quantitative analytics of QuantLib with the R statistical computing environment and language. Most of the changes were made two and four weeks ago: fir...

## Updates to the ‘aqp’ Package for R (version 0.98-3)

November 30, 2010
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Just released an updated version of our 'aqp' package for quantitative soils investigations, available on CRAN and R-Forge. Some of the major changes are listed below: from the aqp NEWS file: -------------------------- aqp 0.98-1 (2010-11-23) --------...

## What’s Next for Revolution R and Hadoop?

November 30, 2010
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It's been a busy fall season for the team at Revolution Analytics. Over the past few months, we've announced major product enhancements for Revolution R -- RevoScaleR, for tackling big data sets, and RevoDeployR, for embedding Revolution R into wider applications. We've continued to add to our growing customer base at an aggressive rate and we've been busy crisscrossing...

## Controlling Amazon Web Services using rJava and the AWS Java SDK

November 30, 2010
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I’ve been messing around with using Amazon Web Services for a while. I’ve had some projects where I wanted to upload files to S3 or fire off EMR jobs. I’ve been controlling AWS services using a hodgepodge of command line tools and the R system() function to call the tools from the command line.

## how to install 64-bit rggobi on Mac OS X 10.5

November 30, 2010
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rggobi is the first package which didn't survive my transition from 32-bit to 64-bit in R 2.11.1. Fortunately, installing the package from source fixes it, and Hadley Wickham has posted the prerequisites and procedure.

## Example 8.16: Exact logistic regression

November 30, 2010
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In example 8.15, on Firth logistic regression, we mentioned alternative approaches to separation troubles. Here we demonstrate exact logistic regression. The code for this appears in the book (section 4.1.2) but we don't show an example of it there. ...

## Sweave Tutorial 3: Console Input and Output – Multiple Choice Test Analysis

November 30, 2010
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This post provides an example of using Sweave to perform an item analysis of a multiple choice test. It is designed as a tutorial for learning more about using Sweave in a mode where console input and output is displayed. Copies of all source code a...

## Sweave Tutorial 3: Console Input and Output – Multiple Choice Test Analysis

November 30, 2010
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This post provides an example of using Sweave to perform an item analysis of a multiple choice test. It is designed as a tutorial for learning more about using Sweave in a mode where console input and output is displayed. Copies of all source code a...

## Hägerstrand Time-Space Cube

November 30, 2010
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With the rgl package it’s possible to interact with the 3d visualization of the timespace tracks. Code example: plot3d(lon,lat,timedate, xlim=range(lon), ylim=range(lat), zlim=range(timedate), ticktype=”detailed”, xlab=”longitude”, ylab=”latitude”, zlab=”Date”, col= as.POSIXlt(daten)\$mday, type=”l”, main=plottitle) In the posted example individual waypoints were added by drawing vertical lines.

## GOSemSim redesign in terms of S4 classes

November 30, 2010
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I started to develop GOSemSim package two years ago when I was not quite familiar with R. I am very happy to see that someone use it and found it helpful. I try to learn S4 and redesign GOSemSim with S4 classes and methods in the pass two weeks, and the very first version was implemented. As I’m not...

## GOSemSim redesign in terms of S4 classes

November 30, 2010
By

I started to develop GOSemSim package two years ago when I was not quite familiar with R. I am very happy to see that someone use it and found it helpful. I try to learn S4 and redesign GOSemSim with S4 classes and methods in the pass two weeks, and the very first version was implemented. As I’m...

## Analysis of retractions in PubMed

November 30, 2010
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As so often happens these days, a brief post at FriendFeed got me thinking about data analysis. Entitled “So how many retractions are there every year, anyway?”, the post links to this article at Retraction Watch. It discusses ways to estimate the number of retractions and in particular, a recent article in the Journal of

## Data visualization videos

November 29, 2010
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Probably everyone has seen Hans Rosling’s famous TED talk by now. I recently came across a couple of other exceptional talks on data visualization: Hans Rosling again: Let my dataset change your mindset. If only all statistics lecturers were this dynamic! David McCandless: The beauty of data visualization. Not so exciting as Hans, but some great

## Initializing the Holt-Winters method

November 29, 2010
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The Holt-Winters method is a popular and effective approach to forecasting seasonal time series. But different implementations will give different forecasts, depending on how the method is initialized and how the smoothing parameters are selected. In this post I will discuss various initialization methods. Suppose the time series is denoted by and the seasonal period

## Sorting out Sweave in Eclipse/StatET

November 29, 2010
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Using Sweave to produce pretty-looking documentation for R is awfully handy. It takes a little tweaking to get set up in Eclipse and StatET though. I followed the information in Jeromy Anglim’s webpage to originally get Sweave set up. The followi...

## Slices and crumbs [arXiv:1011.4722]

November 29, 2010
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$Slices and crumbs [arXiv:1011.4722]$

An interesting note was arXived a few days ago by Madeleine Thompson and Radford Neal. Beside the nice touch of mixing crumbs and slices, the neat idea is to have multiple-try proposals for simulating within a slice and to decrease the dimension of the simulation space at each try. This dimension diminution is achieved via

## The Joy of Visualizations

November 29, 2010
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This is a clip from the forthcoming BBC4 program, The Joy of Stats: The clip shows Hans Rosling (who we've profiled here before), plotting life expectancy versus income for various countries, and animating over time. The clip amply demonstrates that with the right presentation and story, even the simplest of scatterplots can be a joy to behold. I'm looking...

## Altering Eclipse user name

November 29, 2010
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Using StatET’s code generation templates is handy, but the standard Eclipse variable for \${user} just inserts the currently logged-in user’s account name. If you want a different name to appear when \${user} is called, one method is to alter...

## John Chambers on R and Multilingualism

November 29, 2010
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John Chambers, one of the creators of R's predecessor S and a current member of the R Core Group, gave a seminar at Stanford last week titled "R, other languages and object-oriented programming". Unfortunately, I was away for the Thanksgiving break and couldn't make it myself, but John has kindly made his slides (PDF) available for download. The talk...

## John Chambers on R and Multilingualism

November 29, 2010
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John Chambers, one of the creators of R's predecessor S and a current member of the R Core Group, gave a seminar at Stanford last week titled "R, other languages and object-oriented programming". Unfortunately, I was away for the Thanksgiving break and couldn't make it myself, but John has kindly made his slides (PDF) available for download. The talk...

## Statistique de l’assurance STT6705V, partie 11

November 29, 2010
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Last course will be uploaded soon (the links will be here and there). The R code considered is given below. First, we had to work a little bit on the datasets, tabB=read.table("http://perso.univ-rennes1.fr/arthur.charpentier/tabB.csv", sep=";",head...

## SAS and R joins SAS-x

November 29, 2010
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Tal Galili, organizer of the R-bloggers blog aggregator, has opened a new aggregator for people blogging about SAS. If you're unfamiliar with the concept, an aggregator is a single blog which republishes (with permission, in this case) the entries fro...

## INFORMS Data Mining Competition leaders used Open Source software

November 29, 2010
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The results of 2010 INFORMS data mining competition just recently finished.  The leaders were presented at the 2010 Annual INFORMS Conference.  The 2010 INFORMS data mining competition goal was to determine short term movements in stock price...

## INFORMS Data Mining Competition leaders used Open Source software

November 29, 2010
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The results of 2010 INFORMS data mining competition just recently finished.  The leaders were presented at the 2010 Annual INFORMS Conference.  The 2010 INFORMS data mining competition goal was to determine short term movements in stock price...

## Joy of Stats coming soon

November 29, 2010
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The Joy of Stats really is a joy.  It will be shown on BBC4, apparently scheduled for December 7.  (That date comes from Hans Rosling on twitter, I haven’t found scheduling evidence at the BBC.) I saw its debut at the Royal Statistical Society on World Statistics Day. Here is a five minute excerpt: You … Continue reading...

## Sweave Tutorial 2: Batch Individual Personality Reports using R, Sweave, and LaTeX

November 29, 2010
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This post documents an example of using Sweave to generate individualised personality reports based on responses to a personality test. Each report provides information on both the responses of the general sample and responses of the specific respond...

## Sweave Tutorial 2: Batch Individual Personality Reports using R, Sweave, and LaTeX

November 29, 2010
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This post documents an example of using Sweave to generate individualised personality reports based on responses to a personality test. Each report provides information on both the responses of the general sample and responses of the specific respond...