Posts Tagged ‘ programming ’

Matrix determinant with the Lapack routine dspsv

April 6, 2010
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The Lapack routine dspsv solves the linear system of equations Ax=b, where A is a symmetric matrix in packed storage format. However, there appear to be no Lapack functions that compute the determinant of such a matrix. We need to compute the determinant, for instance, in order to compute the multivariate normal density function. The

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BioMart (and biomaRt)

March 26, 2010
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BioMart (and biomaRt)

I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a gene. These are called filters. They have values –

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ECG Signal Processing

March 24, 2010
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ECG Signal Processing

After reading (most of) “The Scientists and Engineers Guide to Digital Signal Processing” by Steven W. Smith, PhD, I decided to take a second crack at the ECG data. I wrote a set of R functions that implement a windowed (Blackman) sinc low-pass filter. The convolution of filter kernel with the input signal is conducted

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ggplot and concepts — what’s right, and what’s wrong

March 7, 2010
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ggplot and concepts — what’s right, and what’s wrong

A few months back I gave a presentation to the NYC R Meetup. (R is a statistical programming language. If this means nothing to you, feel free to stop reading now.) The presentation was on ggplot2, a popular package for generating graphs of data and statistics. In the talk (which you can see here, including

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A Case Study in Optimising Code in R

February 16, 2010
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A Case Study in Optimising Code in R

This post presents an experience I had optimising the efficiency of code for a data analysis task in R. I'm not an expert in programming nor code optimisation. However, I thought my experience might make an interesting case study for others at a simila...

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A new twist on the identifier mapping problem

January 11, 2010
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A new twist on the identifier mapping problem

Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, but that’s apparently way too

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[, [[, $: R accessors explained

October 21, 2009
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[, [[, $: R accessors explained

For more than ten years, I have been teaching R both formally and informally. One thing that I find often trips up students is the use of R’s accessors and mutators. ( For those readers not from a formal computer science background, an accessor is a method for accessing data in an object

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Compiling and Cross-compiling R packages for Windows (win32)

September 3, 2009
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so recently i’m learning how to compile and cross-compile R packages from source for windows machines, which means i have to create windows binaries. the first option is to build on a windows system, and the 2nd is to cross-build on an intel-based linux or mac system. i will outline my experience. Send it off

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R and data

May 26, 2009
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R and data

My fellow bloggers John and Scott have posted recently about the free statistical programming language R.  How does it compare to an expensive language like SAS? If you’ve done any statistical analysis, then you’ll know that getting and cleaning the data is a major step in any project.  SAS does a pretty good job at

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S3 vs S4, efficiency issues

May 23, 2008
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S3 vs S4, efficiency issues

While developing some new simulation code with S4 system I stumbled upon some big difficulties in terms of computational efficiency. That lead me to diging into archives of Rhelp and Rdevel looking for clues. I found some interesting threads that address almost exactly the same problems that I do. Read for yourself here and here,

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