Monthly Archives: July 2012

Fix Overplotting with Colored Contour Lines

July 6, 2012
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Fix Overplotting with Colored Contour Lines

I saw this plot in the supplement of a recent paper comparing microarray results to RNA-seq results. Nothing earth-shattering in the paper - you've probably seen a similar comparison many times before - but I liked how they solved the overplotting...

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Interest Differencing: Folk Commonly Followed by Tweeting MPs of Different Parties

July 6, 2012
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Interest Differencing: Folk Commonly Followed by Tweeting MPs of Different Parties

Earlier this year I doodled a recipe for comparing the folk commonly followed by users of a couple of BBC programme hashtags (Social Media Interest Maps of Newsnight and BBCQT Twitterers). Prompted in part by a tweet from Michael Smethurst/@fantasticlife about generating an ESP map for UK politicians (something I’ve also doodled before – Sketching

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A practical introduction to garch modeling

July 6, 2012
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A practical introduction to garch modeling

We look at volatility clustering, and some aspects of modeling it with a univariate GARCH(1,1) model. Volatility clustering Volatility clustering — the phenomenon of there being periods of relative calm and periods of high volatility — is a seemingly universal attribute of market data.  There is no universally accepted explanation of it. GARCH (Generalized AutoRegressive … Continue reading...

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The R Journal Volume 4/1

July 6, 2012
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The R Journal Volume 4/1

The 'Summer edition' of the R Journal is out! Get it from here.

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automated cell phenotyping — R package “EBImage”

July 5, 2012
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automated cell phenotyping — R package “EBImage”

Counting cells under microscope is always laborious and null. Those in the art would be relieved with assistance of a powerful image processing package, EBImage. Images are treated as “Image” objects, essentially multi-dimensional arrays. The class “Image” contains spatial information, pixel … Continue reading →

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More Exploration of Crazy RUT

July 5, 2012
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More Exploration of Crazy RUT

Unintentionally while playing with the lawstat package in R, I started trying to build systems (STANDARD DISCLAIMER: NOT INVESTMENT ADVICE AND WILL LOSE LOTS OF MONEY SO PROCEED WITH CAUTION) based on the Jarque Bera test of normality (entry in Wikiped...

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A better ‘nls’ (?)

July 5, 2012
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A better ‘nls’ (?)

Those that do a lot of nonlinear regression will love the nls function of R. In most of the cases it works really well, but there are some mishaps that can occur when using bad starting values for the parameters. One of the most dreaded is the “singular gradient matrix at initial parameter estimates” which

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Health Care Costs – Part 1, "The Problem"

July 5, 2012
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Health Care Costs – Part 1, "The Problem"

The ProblemIn the United States, health care costs have been going up for a number of years, even when adjusted for inflation. Not unlike a runaway freight train, this rampant inflation cannot continue indefinitely without crashing....

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New R User Group in Leipzig, Germany

July 5, 2012
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Leipzig R Statistical Computing is the sixth local R user group in Germany, and has been holding meetings since February. In the next meeting on July 12, member Claudia Beleites will talk about her pacakges softclassval (for classifier performance measures) and hyperspec (for hyperspectral data). meetup.com: Leipzig R Statistical Computing

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Validating email adresses in R

July 5, 2012
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I currently program an automated report generation in R – participants fill out a questionnaire, and they receive a nicely formatted pdf with their personality profile. I use knitr, LaTex, and the sendmailR package. Some participants did not provide valid email addresses, which caused the sendmail function to crash. Therefore I wanted some validation of

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