Experiments with igraph

April 21, 2010
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Experiments with igraph

Networks – social and biological – are all the rage, just now. Indeed, a recent entry at Duncan’s QOTD described the “hairball” network representation as the dominant cultural icon in molecular biology. I’ve not had occasion to explore networks “professionally”, but have always been fascinated by both networks and the tools used to analyse them.

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R / Finance 2010 presentations

April 20, 2010
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Last Friday and Saturday the second R / Finance conference took place in Chicago on the UIC campus. As a co-organizer, it was a great pleasure to see so many users of R in Finance---from both industry and academia---come to Chicago to discuss and sh...

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R / Finance 2010 presentations

April 20, 2010
By

Last Friday and Saturday the second R / Finance conference took place in Chicago on the UIC campus. As a co-organizer, it was a great pleasure to see so many users of R in Finance---from both industry and academia---come to Chicago to discuss and shar...

Read more »

R / Finance 2010 presentations

April 20, 2010
By

Last Friday and Saturday the second R / Finance conference took place in Chicago on the UIC campus. As a co-organizer, it was a great pleasure to see so many users of R in Finance---from both industry and academia---come to Chicago to discuss and sh...

Read more »

Book Review – ggplot 2: Elegant Graphics for Data Analysis by Hadley Wickham (Springer 2009)

April 20, 2010
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Book Review – ggplot 2: Elegant Graphics for Data Analysis by Hadley Wickham (Springer 2009)

Order this book from Amazon This book is written by the author of the ggplot2 package for R, which is a package with a design inspired by the grammar of graphics and can remove some of the effort required to put together impressive graphs. The book is just under 200 pages and covers a

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Data I/O performance tips

April 20, 2010
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The R tag on StackOverflow recently topped 1000 questions, and continues to be a great community resource for practical tips on using the R language for data analysis and visualization. To take one example, "Efficiency of operations on R data structures" has been answered with some great tips on efficiently getting data in and out of the R system....

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R and the Next Big Thing

April 19, 2010
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I've been travelling for the past few days (for the R/Finance 2010 conference in Chicago), so I'd missed much of the reaction to AnnMaria De Mars' article last week where she claimed that "R is an epic fail". Understandably, that inflammatory statement provoked many reactions from the R community on Twitter and in the blogosphere. (I suspect the fact...

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A stateful C function for R: parsing Fasta sequences

April 19, 2010
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In the following post, I'll create a C extension for R. This extension will iterate over all the FASTA sequences in a file and will return a pair(name,sequence) for each sequence, that is to say that I won't store all the sequences in memory.The C code...

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A stateful C function for R: parsing Fasta sequences

April 19, 2010
By

In the following post, I'll create a C extension for R. This extension will iterate over all the FASTA sequences in a file and will return a pair(name,sequence) for each sequence, that is to say that I won't store all the sequences in memory.The C code...

Read more »

Converting Alpha-Shapes into SP Objects

April 19, 2010
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Converting Alpha-Shapes into SP Objects

Just read about a new R package called alphahull (paper) that sounds like it might be a good candidate for addressing this request regarding concave hulls. Below are some notes on computing alpha-shapes and alpha-hulls from spatial data and converting the results returned by ashape() and ahull() into SP-class objects. Note that the functions...

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R and Tolerance Intervals

April 19, 2010
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Confidence intervals and prediction intervals are used by statisticians on a regular basis. Another useful interval is the tolerance interval that describes the range of values for a distribution with confidence limits calculated to a particular percentile of the distribution. The R package tolerance can be used to create a variety of tolerance intervals of

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Estimating Missing Data with aregImpute() {R}

April 19, 2010
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  Missing Data Soil scientists routinely sample, characterize, and summarize patterns in soil properties in space, with depth, and through time. Invariably, some samples will be lost or sufficient funds required for complete characterization can run out. In these cases the scientist is left with a data table that contains holes (so to speak) in the rows/columns that are...

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R tip: Maximum screen width

April 19, 2010
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R can be annoying in that even if you stretch your terminal or R GUI session to a whole screen width it will still only show 80 characters width. This can make wide tables really hard to read. options(width=150)Use the options command width to set...

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R tip: Maximum screen width

April 19, 2010
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R can be annoying in that even if you stretch your terminal or R GUI session to a whole screen width it will still only show 80 characters width. This can make wide tables really hard to read. options(width=150)Use the options command width to set...

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Example 7.33: Specifying fonts in graphics

April 19, 2010
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Example 7.33: Specifying fonts in graphics

For interactive data analysis, the default fonts used by SAS and R are acceptable, if not beautiful. However, for publication, it may be important to manipulate the fonts. For example, it would be desirable for the fonts in legends, axis labels, or o...

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Getting your web application and R(Apache) to talk to each other

April 19, 2010
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Getting your web application and R(Apache) to talk to each other

Here’s the situation. Web applications, built using a framework (e.g. Rails, Django) are great for fetching data from a database and rendering it. They’re not so great for crunching and charting the data. Conversely, R is great for crunching and charting, but doesn’t make for a great web application. The idea then, is to let

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Thoughts on LSPM from R/Finance 2010

April 18, 2010
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Thoughts on LSPM from R/Finance 2010

I just got back from R/Finance 2010 in Chicago. If you couldn't make it this year, I strongly encourage you to attend next year. I will post a more comprehensive review of the event in the next couple days, but I wanted to share some of my notes spec...

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Sudokus more random than random!

April 18, 2010
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Sudokus more random than random!

Darren Wraith pointed out this column about sudokus to me. It analyses the paper by Newton and De Salvo published in the Proceedings of the Royal Academy of Sciences A that I cannot access from home. The discussion contains this absurd sentence “Sudoku matrices are actually more random than randomly-generated matrices” which shows how mistreated

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Summarising data using scatter plots

April 18, 2010
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Summarising data using scatter plots

A scatter plot is a graph used to investigate the relationship between two variables in a data set. The x and y axes are used for the values of the two variables and a symbol on the graph represents the combination for each pair of values in the data set. This type of graph is

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alphahull: an R Package for Alpha-Convex Hull

April 16, 2010
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alphahull: an R Package for Alpha-Convex Hull

new paper on the α-convex hull appeared in the Journal of Statistical Software today (http://www.jstatsoft.org/v34/i05/paper). The α-convex hull is an interesting problem which caught my attention long time ago but I didn’t know a solution then. R has a function chull() which can generate (indices of) the convex hull for a series of points. Now

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Significant Figures in R and Rounding

April 16, 2010
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Significant Figures in R and Rounding

This is a follow-on to my previous post about determining significant digits, or sigdigs, in performance and capacity planning calculations. Once we know how to do that, inevitably we will be faced with rounding the result of a calculation to the least...

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Simulating Dart Throws in R

April 16, 2010
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Back in November 2009 Wired wrote an article about some grad students who decided to try to stochastically model throwing darts. Because I don’t actually read printed material I didn’t see the article until a couple of months ago. My immediate thought was, “hey, I drink beer. I throw darts. I build stochastic models. Why

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R Command Line

April 16, 2010
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R Command Line

I am an R user! And I see a whole army of R users, here in defiance of tyranny. You’ve come to use R as free men… and free men you are. What will you do with that freedom? Will you use R? Use R and you may use the command line. Use SAS,

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Because it’s Friday: When infographics go bad

April 16, 2010
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Because it’s Friday: When infographics go bad

Phil Gyford laments crappy infographics swamping the good: Phil Gyford on Flickr: Infographic (used under Creative Commons license)

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R – not the epic fail we thought

April 16, 2010
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I usually like AnnMaria's witty insight. I can relate to a lot of what she is saying. After all SAS and family life are large parts of my life, too. But you can imagine the reaction she provoked in saying the following:I know that R is free and I am ac...

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Rcpp 0.7.12

April 16, 2010
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A new bug fix versions 0.7.12 of Rcpp is awaiting inclusion into CRAN and Debian. It is also available from here. This is another bug-fix version related solely to a build failure on Windows. Trying to protect paths with spaces has the side-effect of ...

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Rcpp 0.7.12

April 16, 2010
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A new bug fix versions 0.7.12 of Rcpp is awaiting inclusion into CRAN and Debian. It is also available from here. This is another bug-fix version related solely to a build failure on Windows. Trying to protect paths with spaces has the side-effect...

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An article attacking R gets responses from the R blogosphere – some reflections

April 16, 2010
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An article attacking R gets responses from the R blogosphere – some reflections

In this post I reflect on the current state of the R blogosphere, and share my hopes for the future

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The Next Big Thing: SAS and SPSS!…wait, what?

April 15, 2010
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The Next Big Thing: SAS and SPSS!…wait, what?

Thanks to the R Bloggers aggregator I came across Yihui Xie’s post on a piece currently making the rounds about statistical analysis platforms. In The Next Big Thing, AnnMaria De Mars makes the argument that R—as a statistical computing platform—is not well suited for what she views as the next big things in data

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