Compressed Sensing with R

October 15, 2012
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Compressed Sensing with R

Compressed sensing (CS) is pretty much appealing all current signal processing research community. At the same time, popularity of R language gaining a strong foot in the research and industry. Even though historically MATLAB is a de-facto standard in ...

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Review of “R For Dummies”

October 15, 2012
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Review of “R For Dummies”

The authors are Andrie de Vries and Joris Meys. Executive summary Pretty much all I’d hoped for — and I had high hopes. Significance The “Dummies” series is popular for introducing specific topics in an inviting way. R For Dummies is a worthy addition to the pack. There is a competitor by the name of … Continue reading...

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Annotations for “R For Dummies”

October 15, 2012
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Annotations for “R For Dummies”

Here are detailed comments on the book.  Elsewhere there is a review of the book. How to read R For Dummies In order to learn R you need to do something with it.  After you have read a little of the book, find something to do.  Mix reading and doing your project. You cannot win … Continue reading...

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Banking to n degrees

October 15, 2012
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Banking to n degrees

As often happens, I have learned of a technique just as it is being called into question. In this case, the technique is changing the aspect ratio of a line plot such that the typical slope of each segment is 45° (see), a rule of thumb which has bee...

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Using consistent R and LaTeX fonts in Org (or knitr, or Sweave)

October 15, 2012
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Using consistent R and LaTeX fonts in Org (or knitr, or Sweave)

I love good typography, even more so as Microsoft Word and PowerPoint have debased our standards. When I see a really fine piece of technical typesetting, it’s almost always done using TeX and friends. Beautiful LaTeX documents are easy to … Continue reading →

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How do I re-arrange…?: Ordering a plot.

October 15, 2012
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How do I re-arrange…?: Ordering a plot.

One of the most widely seen FAQ coming across list serves and R help sites is the question: “How do I re-arrange/re-order (plotting geom/aesthetic such as bar/labels) in a (insert plot type here) using(insert graphics system here) in R?” . … Continue reading →

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Fixing non positive definite correlation matrices using R

Problem When a correlation or covariance matrix is not positive definite (i.e., in instances when some or all eigenvalues are negative), a cholesky decomposition cannot be performed. Sometimes, these eigenvalues are very small negative numbers and occur due to rounding or due to noise in the data. In simulation studies a known/given correlation has to be imposed on an input...

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2012-7 A Structured Approach for Generating SVG

October 14, 2012
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The gridSVG package exports grid images to an SVG format for viewing on the web. This article describes a new development in the way that gridSVG produces the SVG output. The result is greater flexibility in how the SVG output … Continue reading →

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New version of httr: 0.2

October 14, 2012
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New version of httr: 0.2

We’re happy to announce a new version of httr, a package designed to make it easy to work with web APIs. Httr is a wrapper around RCurl, and provides: functions for the most important http verbs: GET, HEAD, PATCH, PUT, DELETE and POST. automatic cookie handing across requests, connection sharing, and standard SSL config. a

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Rcpp 0.9.15

October 14, 2012
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Rcpp release 0.9.15 is now on CRAN and being uploaded to Debian. Martin Morgan provided a clever fix for a header search needed between clang++ (especially on OS X) and g++ (which still provided libstdc++ and headers for clang++). This should hopefu...

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A very quick introduction to ggplot2

October 14, 2012
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A very quick introduction to ggplot2

I gave a very brief 10mn introduction to ggplot2 at the Birmingham R user group meeting on Monday. The aim was to give a headstart to R users who’ve heard of ggplot2 but never got around to trying it. I … Continue reading →

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Putting a football model into JAGS

October 14, 2012
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Putting a football model into JAGS

In this post the football model is programmed into JAGS. There are all the reasons to do so. Jags 3.3 is recently released, I was stimulated by Gianluca's post . Obviously I could copy the model in his paper, but that would be too easy a...

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Dark matter benchmarks: All over the map

October 14, 2012
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Dark matter benchmarks: All over the map

The three benchmark algorithms for predicting the location of dark matter halos are, for the most part, all over the map. Most of the test skies look something like this: There are, however, some skies with rather strong halo signals that get a decent amount of agreement: The Lenstool MLE algorithm is the current state

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Vice Presidential Debates with qdap-beta

October 13, 2012
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Vice Presidential Debates with qdap-beta

After the presidential debates I used the beta version of qdap to provide some initial surface level analysis (LINK to Presidential Debates with qdap-beta). In the comments of that post, annon (a commenter) provided a link to an analysis/visualization that … Continue reading →

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Observing Dark Worlds – Visualizing dark matter’s distorting effect on galaxies

October 13, 2012
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Observing Dark Worlds – Visualizing dark matter’s distorting effect on galaxies

Some people like to do crossword puzzles. I like to do machine learning puzzles. Lucky for me, a new contest was just posted yesterday on Kaggle. So naturally, my lazy Saturday was spent getting elbow deep into the data. The training set consists of a series of ‘skies’, each containing a bunch of galaxies. Normally,

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The unicorn problem

October 13, 2012
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The unicorn problem

Let’s say your goal is to observe all known species in a particular biological category. Once a week you go out and collect specimens to identify, or maybe you just bring your binoculars to do some spotting. How long will it take you to cross off every species on your list? I’ve been wondering this

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The movement of a drunk guy – Random Walk and exponential regression

October 13, 2012
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The movement of a drunk guy – Random Walk and exponential regression

I was in a party last night and a guy was totally drunk. Not just the guy who had a few drinks and speaks a bit too loud, but the one who is not very likely to remember what he has done during his night, but who is rather very likely to suffer from a h...

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Agreement between code readability ratings given by students

October 13, 2012
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Agreement between code readability ratings given by students

I have previously written about how we know nothing about code readability and questioned how the information content of expressions might be calculated. Buse and Weimer ran a very interesting experiment that asked subjects to rate short code snippets for readability (somebody please rerun this experiment using professional software developers). I’m interested in measuring how

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Overfitting

October 13, 2012
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Overfitting

What do you think when you see a model like the one below? Does this strike you as a good model? Or as a bad model? There’s no right or wrong answer to this question, but I’d like to argue that models that are able to match white noise are typically bad things, especially when

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How to choose the right *apply function

October 13, 2012
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How to choose the right *apply function: This is an amazing stackoverflow answer to help you decide which of the many *apply functions (apply, lapply, sapply, vapply, mapply, rapply, tapply) is appropriate for the task at hand. I’m planning on doing...

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Compound Poisson and vectorized computations

October 12, 2012
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Compound Poisson and vectorized computations

Yesterday, I was asked how to write a code to generate a compound Poisson variables, i.e. a series of random variables  where  is a counting random variable (here Poisson disributed) and where the 's are i.i.d (and ind...

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Minute by Minute Twitter Sentiment Timeline from the VP debate

October 12, 2012
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Minute by Minute Twitter Sentiment Timeline from the VP debate

Click on above graph to enlarge. Background The data for this graph was collected automatically every ~60 seconds of the VP debate on 10/11/2012, with an ending aggregate sample size of 363,163 tweets.  From this dataset duplicate tweets were removed (because of bots), which gave a final dataset of 81,124 remaining unique tweets (52,303-Biden, 28,821-Ryan).

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Color Palettes in HCL Space

October 12, 2012
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Color Palettes in HCL Space

This is a quick follow-up to my previous post about Color Palettes in RGB Space. Achim Zeileis had commented that, perhaps, it would be more informative to evaluate the color palettes in HCL (polar LUV) space, as that spectrum more accurately describes how humans perceive color. Perhaps more clear trends would emerge in HCL space,

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Creating SVG Plots from R

October 12, 2012
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I recently wanted to create a ggplot that I could then 'tweak' furthur. This is my solution, to create an .svg file which can be loaded into a suitable application (I prefer Inkscape) and furthur edited / tweaked. # Build an example Plotlibrary(ggplot2...

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Deploy Rook Apps: Part II

October 12, 2012
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In Part I, I described how you can deploy your Rook applications with rApache. This post describes how you can do it with R itself. But before we get into that, I’d like to explain the off-again on-again relationship Rook has had with CRAN, R&#82...

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Nine lightning talks on R

October 12, 2012
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At Tuesday's Bay Area R User Group meetup, nine speakers gave five-minute talks on various aspects of R. Revolution Analytics' Luba Gloukhov was one of the presenters, and also provides the summary of the talks below. Links to the slides are included where available for you to check out. Ariel Faigon: Chrestomathy with R Ariel walked us through his...

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Overlay of design matrices in genetic analysis

October 12, 2012
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Overlay of design matrices in genetic analysis

I’ve ignored my quantitative geneticist side of things for a while (at least in this blog) so this time I’ll cover some code I was exchanging with a couple of colleagues who work for other organizations. It is common to … Continue reading →

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Using cairographics with ggsave()

October 12, 2012
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Using cairographics with ggsave()

Whenever possible, I try to save R graphic output in a vector format, typically pdf(). I also like to use the handy ggsave() function to do so, as it streamlines the process, and makes it easy to be consistent across formats. However, at times it is n...

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Loading SPSS (.sav) into Stata

October 11, 2012
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Most statistical softwares nowadays are able to convert their files to a wide range of other packages. Perhaps it is the reason for the discontinuity of old converter bundles like SAS Transport and DBMS. Interesting, however, Stata, a quite popular statistical package, still lack built-in support for exporting and importing files among concurrent softwares like

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