JAGS 3.1.0

August 11, 2011
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JAGS 3.1.0

The patch release, 3.1.0  fixes a problem due to a change in the way the adapt command works (and the adapt() function in rjags).  If the model has an adaptive phase, you should normally include a burn in period (with … Continue reading →

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System Failure-Maybe it Will Help

August 11, 2011
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System Failure-Maybe it Will Help

I hope everyone is enjoying the market.  After a crazy week personally and 6% intraday swings, I remember why I abandoned day trading. I often wonder if I should share ideas that do not work as well as I would like.  In this case, I know I ha...

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Setup up the inverse of additive relationship matrix in R

August 11, 2011
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Setup up the inverse of additive relationship matrix in R

Additive genetic covariance between individuals is one of the key concepts in (quantitative) genetics. When doing the prediction of additive genetic values for pedigree members, we need the inverse of the so called numerator relationship matr...

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FastCompany on telling stories with data

August 11, 2011
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An article in FastCompany today profiles two websites that excel in telling engaging stories with data: the FlowingData and OkTrends blogs. Both sites often use R for data analysis and data visualization, and have been featured here on this blog. FlowingData regularly posts guides on how to use R to recreate many of its featured visualizations with bubble charts,...

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OpenAnalytics at UseR!2011

August 11, 2011
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Thursday 11 August 2011 - 22:36 OpenAnalytics is happy to sponsor UseR!2011 and will present recent work that has been released under open source license in three presentations: R and GPU Computing, which accompanies the first public release of...

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High-Performance in Cloud Computing

August 11, 2011
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High-Performance in Cloud Computing

Very often scientists are worried about performance and security in cloud computing. Especially, when talking about High-Performance Computing (HPC) in the cloud it is a very important aspect to proof efficient calculation speed in the cloud. Cloud computing describes a new delivery model for IT services based on Internet protocols, and it typically involves provisioning

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Using OpenMP-ized C code with R

August 11, 2011
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What is OpenMP? Basically a standard compiler extension allowing one to easily distribute calculations over multiple processors in a shared-memory manner (this is especially important when dealing with large data — simple separate-process approach usually requires as many copies of the working data as there are threads, and this may easily be an overkill even

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Test Difference between Two Proportions & Plot Confidence Intervals

August 11, 2011
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Test Difference between Two Proportions & Plot Confidence Intervals

..an illustrative example for testing proportions and presenting the results.the data: number of indigenous and alien plant species with and without vegetative reproduction. Hypothesis: The proportion of species with vegetative reproduction is differen...

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ggplot2: Determining the order in which lines are drawn

August 11, 2011
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ggplot2: Determining the order in which lines are drawn

In a time series, I want to plot the values of an interesting cluster versus the background. However, if I'm not careful, ggplot will draw the items in an order determined by their name, so background items will obscure the interesting cluster: Corr...

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Build multiarch R (32 bit and 64 bit) on Debian/Ubuntu

August 11, 2011
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I have the 64 bit version of R compiled from source on my Ubuntu laptop. I recently had a need for R based on 32 bit since a package I needed to compile and use only works in 32 bit. I thought it was readily available on Ubuntu since both 32 bit and 64 bit... Read more »

Plotting Cumulative FII & DII Inflow against Nifty spot index

August 10, 2011
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Plotting Cumulative FII & DII Inflow against Nifty spot index

Now that I have the FII and DII Inflow along with Nifty Index, I tried my hands on charting!The objective is to plot the Cumulative FII, DII and Net Inflow and Nifty Index for current year (2011) on a single graph. This post takes inspiration from Deep...

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Analysis of Japanese Earthquakes Data

August 10, 2011
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Analysis of Japanese Earthquakes Data

Latest version is here.Greater attention is much more about earthquakes, Touhoku earthquake has occurred on March 11, 2011. Earthquake data are released at Japan Weather Association's Tenki.jp. We can get these variables from the site.Date, TimeAreaLat...

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Climate datasets in R

August 10, 2011
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As an ecologist working on climate change questions, I’ve always found it rather tedious to acquire and process climate data, especially when dealing with large spatiotemporal scales. Although many agencies provide free access to climate data, there is often some overhead (typically one to two days) before the data are made available for download via

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By: Build multiarch R (32 bit and 64 bit) on Debian/Ubuntu

<p> have the 64 bit version of R compiled from source on my Ubuntu laptop. I recently had a need for R based on 32 bit since a package I </p>

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Error : package does not have a name space

August 10, 2011
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Error : package does not have a name space

Here is a frustrating knot I am beginning to unravel. R has a namespace structure to help reduce errors resulting from functions, methods, objects, classes having the same name from two different packages. Makes sense. Those R objects that are … Continue reading →

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In case you missed it: July Roundup

August 10, 2011
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In case you missed them, here are some articles from July of particular interest to R users. A simulation in R finds the value (or disadvantage) or drawing an X, J, Q or Z in Scrabble. How to display high-quality graphics on the web using SVG output from R. A review of Paul Murrell's talk about raster image support...

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Bayes factors and martingales

August 10, 2011
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Bayes factors and martingales

A surprising paper came out in the last issue of Statistical Science, linking martingales and Bayes factors. In the historical part, the authors (Shafer, Shen, Vereshchagin and Vovk) recall that martingales were popularised by Martin-Löf, who is also influential in the theory of algorithmic randomness. A property of test martingales (i.e., martingales that are non

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SNA: Visualising an email box with R

August 10, 2011
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SNA: Visualising an email box with R

Are statistics sexy? Visualising social networks certainly is! I wrote a little function, which makes producing beautiful plots depicting a mailbox with R an extremely easy task. I find visualisations of ‘social graphs’ particularly appealing. They look like flowers. I … Continue reading →

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Dump MySQL to CSV using R

August 10, 2011
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Based on a related post on one of my favorite python-lists I remembered, that I wrote a similar snipplet some time ago. So if you want to dump your whole MySQL database to csv-files you can recycle the following code: ?Download mysql2cvs.R1 2 3 4 5 6 7 8 9 require(RMySQL) m<-MySQL() summary(m) con<-dbConnect(m, dbname

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Using the google prediction API from R

August 10, 2011
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Using the google prediction API from R

Google has a "black box" prediction API that they provide for use with creating recommender systems or filtering spam. Furthermore, they provide an R package for interfacing that API, but try as I might I cannot get it to work under windows. Here are ...

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Plotting molecular properties for (sub)sets

August 10, 2011
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Plotting molecular properties for (sub)sets

For a toxicology paper we are writing up, I need to create a few plots showing how the toxic and non-toxic molecules differ (or not) with respect to a few molecular properties, such as logP or the molecular weight. The rcdk package provides all, of cou...

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A 60-second survey for R users

August 10, 2011
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I'm doing a little research to validate estimates of the size of the R user community. If you're an R user, please take a minute to complete this three-question survey on R usage at your organization. Thanks in advance. Revolution Analytics: R user base survey

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Informational Easing: A Change In F.O.M.C. Expectations

August 10, 2011
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Informational Easing: A Change In F.O.M.C. Expectations

Let's analyze the latest FOMC policy move.The FOMC met yesterday and changed up the communications strategy.  How so? Well, until yesterday the statement has been saying as of June 22, 2011:"The Committee continues to anticipat...

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Scraping web data in R

August 10, 2011
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Scraping web data in R

In my last post, I went through a lot of effort to scrape the PMI index off the ISM website.  It turns out that was unnecessary effort, as commentator "senne" pointed out that this index is available from FRED, with the symbol NAPM. &nbs...

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Using a “pure infographic” to explore differences between information visualization and statistical graphics

August 10, 2011
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Using a “pure infographic” to explore differences between information visualization and statistical graphics

Our discussion on data visualization continues. One one side are three statisticians–Antony Unwin, Kaiser Fung, and myself. We have been writing about the different goals served by information visualization and statistical graphics. On the other side are graphics experts (sorry for the imprecision, I don’t know exactly what these people do in their day jobs The post Using...

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Multiple cores in R, revisited

August 10, 2011
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The bigmemory package in combination with doMC provides at least a partial solution for sharing a large data set across multiple cores in R. With this solution you can work on the same matrix using several threads. It is also a very scalable solution. ...

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Coding, GUIs and Statistical Rituals

August 10, 2011
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Coding, GUIs and Statistical Rituals

I was recently inspired to comment on this blog post, asking is R is a cure for ‘mindless statistics’. Anyone whose familiar with statistics used in applied fields like epidemiology, sociology, social sciences generally will be familiar with the idea of a ‘statistical ritual’. Rather than think about the proper statistical approach to every question,

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What do you want to see at useR 2012?

August 9, 2011
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This year's useR! conference at Warwick University is less than a week away, but planning is already underway for useR! 2012, to be held at Vanderbilt University in Nashville. If you're planning to attend, conference organizer Frank Harrell is looking for your input: The 2012 R User Conference - useR! 2012 - will be held in Nashville Tennessee USA,...

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Amazon Machine Image Created With RTextTools Pre-installed

We recently created an AMI for Amazon's EC2 cloud computing service. Users with AWS accounts can access the public AMI by searching ami-817eb8e8. The AMI is based off of Drew Conway's excellent AMI, but with R 2.13 loaded and RTextTools and

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