Posts Tagged ‘ programming ’

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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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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R is an Epic Fail?

April 15, 2010
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I came across this blog post just now: The Next Big Thing, and of course these words caught my attention: However, for me personally and for most users, both individual and organizational, the much greater cost of software is the time it takes to install it, maintain it, learn it and document it. On

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I’d be more than happy with the unlinked data web

April 14, 2010
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I’d be more than happy with the unlinked data web

Visit this URL and you’ll find a perfectly-formatted CSV file containing information about recent earthquakes. A nice feature of R is the ability to slurp such a URL straight into a data frame: quakes <- read.csv("http://neic.usgs.gov/neis/gis/qed.asc", header = T) colnames(quakes) # "Date" "TimeUTC" "Latitude" "Longitude" "Magnitude" "Depth" # number of recent quakes nrow(quakes) #

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Plotting “time of day” data using ggplot2

April 14, 2010
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Plotting “time of day” data using ggplot2

William asks: How can I make a graph that looks like this, “tweet density” style, showing time intervals? He then helpfully describes his input data: a CSV file with headers “time started, time finished, date”. Here’s a simple CSV file, tasks.csv: task,date,start,end task1,2010-03-05,09:00:00,13:00:00 task2,2010-03-06,10:00:00,15:00:00 task3,2010-03-06,11:00:00,18:00:00 task4,2010-03-07,08:00:00,11:00:00 task5,2010-03-08,14:00:00,17:00:00 task6,2010-03-09,12:00:00,16:00:00 task7,2010-03-10,14:00:00,19:00:00 task8,2010-03-11,09:30:00,13:30:00 Read into R, calculate the

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Seamless R Extensions using Rcpp and RInside

April 7, 2010
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I just added a new video to the R repository, and this one comes from the Los Angeles R Meetup. The folks in LA were fortunate enough to have Dirk Eddelbuettel—renowned R expert and StackOverflow super-user—discuss his joint work with Romain François for interfacing C++ and R code using the Rcpp package. For those

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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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