Posts Tagged ‘ programming ’

Higher Order Functions in R

September 23, 2010
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Introduction Because R is, in part, a functional programming language, the ‘base’ package contains several higher order functions. By higher order functions, I mean functions that take another function as an argument and then do something with that function. If you want to know more about the usefulness of writing higher order functions in general,

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Namespaces and name conflicts

August 31, 2010
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Namespaces and name conflicts

R packages ‘igraph’ and ‘network’ are good examples of two R packages providing similar but complementary functionalities for which there are a lot of name conflicts. As for now the ‘igraph’ package has a namespace while the ‘network’ package (version 1.4-1) does not. This became an issue when I was working on the ‘intergraph‘ package.

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From igraph to network and back again

August 25, 2010
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From igraph to network and back again

In an effort to achieve this (last paragraph), I created a couple of functions to coerce networks as ‘igraph’ objects to networks as ‘network’ objects and vice versa. I wrapped them into a package called ‘intergraph’ which I just uploaded to my personal miniCRAN. Please mind, this is still an experimental version! Might be bug-infested.

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Tools for Hacking R: Git + Subversion

August 24, 2010
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In an earlier post, I discussed how to use Subversion to download, edit, and generate a patch against R‘s source code. Since most of us can’t commit our code changes back to R‘s repository, we can consider alternatives to store and maintain our patch, until it is eventually incorporated into R. Of course, our changes

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Tools for Hacking R: Subversion

August 23, 2010
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The development version of R is stored in a Subversion repository at the URL http://svn.r-project.org/R/trunk/. In fact, you can browse the source code by clicking the link. Subversion Hierarchy Subversion is software for source code revision control. That means it keeps track of changes, who made them, when they were made, and any comments about

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Abstract word clouds using R

August 23, 2010
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Abstract word clouds using R

A recent question over at BioStar asked whether abstracts returned from a PubMed search could easily be visualised as “word clouds”, using Wordle. This got me thinking about ways to solve the problem using R. Here’s my first attempt, which demonstrates some functions from the RCurl and XML packages. update: corrected a couple of copy/paste

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Ed Burnette on Software Patents

August 17, 2010
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Ed Burnette makes a point that hits home, with regard to software patents, and how engineers and programmers of modern companies are now being asked to write them: Unfortunately, the joke is on all of us. It’s on our economy, as we let patents choke down innovation and increase fear, uncertainty, and doubt in an

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R Environments for Gibbs Sampler State

August 10, 2010
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R Environments for Gibbs Sampler State

I recently decided to revisit some R code that implements a Gibbs sampler in an attempt to decrease the iteration time. My strategy was to implement the sampler state as an R environment rather than a list. The rationale was that passing an environment to and from functions would reduce the amount of duplication (memory

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A tty Connection for R

July 26, 2010
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I completed (some time ago) an initial version of a patch for R, version 2.11.1, that adds a POSIX tty connection. The patch is confirmed to compile and works on Mac OS X (thanks to Ashwin Bhat of Georgia Tech) and Debian GNU Linux. However, it should be portable to other POSIX compliant operating systems.

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Documenting R‘s Connections Internals

July 16, 2010
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Documenting R‘s Connections Internals

In studying R‘s connections source code, I’ve put together a series of notes about their workings. Rather than let the notes go where most of my notes go (I have no idea ), I decided to do some proofreading and make the notes available to others who might be interested. These notes should make the

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