Data Visualization and R Programming Books (Updated)

January 7, 2010
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Download "Getting Started with the Social Media Analytics Research Toolkit" (pdf, 1.25 megabytes) Download the Social Media Analytics Research Toolkit Download Code Like A Pirate - The #rstats Appliance from the SUSE Gallery Disclosure As you probably ...

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Samples per series/dataset in the NCBI GEO database

January 7, 2010
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Samples per series/dataset in the NCBI GEO database

Andrew asks: I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere? At work, we joke that GEO is the only database where data goes in,

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Typos in Chapter 3

January 7, 2010
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Typos in Chapter 3

Here are two more typos in the exercises of Chapter 3 of “Introducing Monte Carlo Methods with R”. – due to the (later) inclusion of an extra-exercise in the book, the “above exercise” in Exercise 3.5 actually means Exercise 3.3. – in Exercise 3.11, question c, a line got commented by mistake in the LaTeX file and

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R’s exponential package growth, ctd.

January 7, 2010
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R’s exponential package growth, ctd.

Reader SK has collected the most recent data on R's package growth, through the latest 2.10 release. The three most recent releases fall slightly below the exponential growth line, which isn't altogether surprising (that's a lot of growth to sustain!). Another interesting thing to look at would be the combined rate of new packages submitted to CRAN and packages...

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Survey question biases and crowdsourcing

January 7, 2010
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It's common knowledge that the way you ask a question in a survey can bias the results you get. (It's been a staple of political pollsters since the dawn of time.) But Aaron Shaw from Dolores Labs has used an interesting technique to demonstrate that bias: crowdsourcing. He asked the same question of crowdsourced respondents assigned randomly to one...

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subsetting a matrix/array in R

January 7, 2010
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From the R-devel svn log. Nice addition… r50896 | falcon | 2010-01-05 12:05:31 -0800 (Tue, 05 Jan 2010) | 7 lines Changed paths: M /trunk/NEWS M /trunk/src/include/Defn.h M /trunk/src/library/base/man/Extract.Rd M /trunk/src/main/subassign.c M /trunk/src/main/subscript.c M /trunk/src/main/subset.c M /trunk/tests/Makefile.common A /trunk/tests/array-subset.R Allow n-dim arrays to be subsetted by an n-column character matrix The character matrix is converted

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Scatter plot with 4 axes labels and grid

January 7, 2010
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Scatter plot with 4 axes labels and grid

Ravi from this post (via Revolutions blog) wanted to check the code that produces the left panel of the Figure 3 from this article taken from the current issue of the R Journal. Below my attempt to reproduce the plot: rv <- seq(1.3, 2.9, .1)...

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Scatter plot with 4 axes labels and grid

January 7, 2010
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Scatter plot with 4 axes labels and grid

Ravi from this post (via Revolutions blog) wanted to check the code that produces the left panel of the Figure 3 from this article taken from the current issue of the R Journal. Below my attempt to reproduce the plot: rv <- seq(1.3, 2.9, .1)...

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R Journal, Volume 1/2, December 2009

January 7, 2010
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The issue 1/2 of the R Journal has been published. It features an article that I co-authored with Spencer Graves and Sundar Dorai-Raj about the sospackage.

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3d scatter plot using R

January 6, 2010
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3d scatter plot using R

The other day I saw a three dimensional scatterplot in Montgomery's Regression book. I wanted to redraw the graph using the provided data. A simple google search revealed that there is a package called scatterplot3d. The scatterplot3d() can be used to draw a 3-dimensional scatter plot. Here is what the steps are: Download and install the package from your nearest...

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3d scatter plot using R

January 6, 2010
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3d scatter plot using R

The other day I saw a three dimensional scatterplot in Montgomery's Regression book. I wanted to redraw the graph using the provided data. A simple google search revealed that there is a package called scatterplot3d. The scatterplot3d() can be used to draw a 3-dimensional scatter plot. Here is what the steps are: Download and install the package from your nearest...

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Programming a custom Backtest Profile in R

January 6, 2010
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Programming a custom Backtest Profile in R

One of the many issues with systems trading is trying to make sense of the vast amounts of data you accumulate with the backtest of a system. Historical backtesting is the first step in testing your trading idea. If it is a trading idea that ought to w...

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RInside release 0.2.1

January 6, 2010
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The shiny new 0.2.1 release of RInside, a set of convenience classes to facilitate embedding of R inside of C++ applications, just went out to CRAN; sources are also at my RInside page This is a maintenance release building on the recent 0.2.0 rel...

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RInside release 0.2.1

January 6, 2010
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The shiny new 0.2.1 release of RInside, a set of convenience classes to facilitate embedding of R inside of C++ applications, just went out to CRAN; sources are also at my RInside page This is a maintenance release building on the recent 0.2.0 release...

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RInside release 0.2.1

January 6, 2010
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The shiny new 0.2.1 release of RInside, a set of convenience classes to facilitate embedding of R inside of C++ applications, just went out to CRAN; sources are also at my RInside page This is a maintenance release building on the recent 0.2.0 rel...

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New Features in ggplot2 0.8.5

January 6, 2010
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Learning R blog details some of the new features in the latest update to ggplot2. The latest version includes functions to make it easier to change axis and legend labels, as well as a function to easily set the limits of the plot display outside the range of the data. Be sure to check back next week - I'm putting...

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Earthquake maps

January 6, 2010
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Earthquake maps

There's been a number of earthquakes in the Solomon Islands over the past few days, including one that caused a tsunami to partially destroy the village of Baniata on Rendova, Western Provence. You can see exactly how many earthquakes have occurred the...

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Earthquake maps

January 6, 2010
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Earthquake maps

There's been a number of earthquakes in the Solomon Islands over the past few days, including one that caused a tsunami to partially destroy the village of Baniata on Rendova, Western Provence. You can see exactly how many earthquakes have occurred the...

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New Features in ggplot2 version 0.8.5

January 6, 2010
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New Features in ggplot2 version 0.8.5

Just before Christmas ggplot2 version 0.8.5 was released, closely following the release of version 0.8.4 a week or so earlier. Whilst both versions included included numerous bugfixes (25 in 0.8.4 and 17 in 0.8.5), the latest version also incorporated some new features. As ggplot2 is all about graphical display, so I went through the list

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The number of R packages is growing exponentially

January 6, 2010
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The number of R packages is growing exponentially

The second issue of the R Journal is out now, and in addition to a bevy of contributed articles and some news from the R Core Group on the new help system introduced in R 2.10, there's an invited section called, intriguingly, "The Future of R". In that section John Fox provides an exhaustively researched and insightful review of...

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R AnalyticFlow

January 6, 2010
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R AnalyticFlow

R AnalyticFlow is an interesting piece of software. From its web site:"R AnalyticFlow is a software which enables state-of-the-art data analysis by drawing analysis flowcharts. You can effectively share processes of data analysis in collaborative wo...

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Latin squares design in R

January 6, 2010
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Latin squares design in R

The Latin square design is used where the researcher desires to control the variation in an experiment that is related to rows and columns in the field.Remember that: * Treatments are assigned at random within rows and columns, with each treatment once per row and once per column. * There are equal numbers...

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Latin squares design in R

January 6, 2010
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Latin squares design in R

The Latin square design is used where the researcher desires to control the variation in an experiment that is related to rows and columns in the field.Remember that: * Treatments are assigned at random within rows and columns, with each treatment once per row and once per column. * There are equal numbers...

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littler 0.1.3

January 5, 2010
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A new littler release (now at 0.1.3) just went out of the door this evening. littler provides r (pronounced littler), a shebang / scripting / quick eval / pipelining front-end to the the R language and system. This version adds a few minor behind-...

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littler 0.1.3

January 5, 2010
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A new littler release (now at 0.1.3) just went out of the door this evening. littler provides r (pronounced littler), a shebang / scripting / quick eval / pipelining front-end to the the R language and system. This version adds a few minor behind-the...

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littler 0.1.3

January 5, 2010
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A new littler release (now at 0.1.3) just went out of the door this evening. littler provides r (pronounced littler), a shebang / scripting / quick eval / pipelining front-end to the the R language and system. This version adds a few minor behind-...

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Typos in Chapter 2

January 5, 2010
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Typos in Chapter 2

When grading homeworks for my Monte Carlo graduate class, I found that my students had pointed out two typos in the exercises of Chapter 2 of “Introducing Monte Carlo Methods with R”. – In Exercise 2.17, question d. should be “d. Show that the maximum of is attained at .“ – In Exercise 2.21, in item

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Transitions and transversions in R

January 5, 2010
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Transitions and transversions in R

A couple of months ago I wrote the following R function to calculate the number of transitions and transversions between DNA sequences in an alignment. The function is fairly slow (an alignment of ~100 sequences, 800 bp in length takes around 30 second...

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Setting the HTML title tag in SAS ODS (the right way)

January 5, 2010
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Setting the HTML title tag in SAS ODS (the right way)

In our department and various places on the Intertubes, SAS programmers set the HTML title tag (which sets the title in web browsers and on search engines) in ODS using the headtext option: ods html headtext="<title>My great report</title>" /* wrong! */ file="foo.html"; This may work in some situations, but it’s ugly and wrong. To see

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