igraph is one of the most popular network analysis packages available. It has official interfaces for C, Python and R, and several other unofficial ones. IGraph/M is an effort to create a polished, well-intergrated and easy to use Mathematica interface for igraph.

It has been half a year since we left Indiana and I miss our trips to the sand dunes of Lake Michigan. This video was shot at the end of January, 2015, around St. Joseph and New Buffalo, Michigan. The piano music is by Monica Xiao.

Mathematica is an excellent and flexible visualization tool, and even supports displaying complex mathematical formulae. However, its typesetting quality is not on par with \(\mathsf{\LaTeX}\). The visual style is not a good match for inclusion in LaTeX documents either. To improve the quality of my figures, I wrote a …

When extending Mathematica through C or C++ code using the LibraryLinkAPI, one common annoyance is that it’s not possible to see messages that the C code sends to stdout or stderr when using the graphical interface. While there are ways to send output directly to the active Mathematica notebook, often the C code is not written to be used exclusively with Mathematica and it simply prints debug messages to stderr. Standard C assertion failures also cause messages to be printed to stderr.

Here I will show how to view the Mathematica kernel’s output in a terminal window, even when using the graphical notebook interface.
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RLink is a standard Mathematica package for accessing R functionality from Mathematica. This is a guide on how to set up RLink with arbitrary R installations on various operating systems and various versions of Mathematica.

For some Friday fun, here’s a word cloud generated from my Mendeley library. It’s based on a collection of about 400 PDF files, the papers I read for my research. Neutral ecology is a bit overrepresented as I used to maintain a Mendeley group on the topic, but …

Have you ever wanted to quickly import some tabular data for quick-and-dirty analysis, either from the web, rich text document, part of a spreadsheet, etc., but then gave up because it seemed too much trouble? This is something I want to do quite frequently, so I wrote a small utility …

I wrote this short tutorial on memoization years ago. Since it turned out to be somewhat popular, and my old website is going away, I am reproducing it here.

Memoization is a very well known programming pattern in Mathematica. Memoization is an optimisation technique: it means making a function “remember …

September 2015 update:If you are looking to use igraph from Mathematica, also take a look at the work-in-progress project IGraph/M. I now recommend using IGraph/M instead of IGraphR except when it does not yet have the functions you need.

Most people I know in academia have personal websites—it’s expected. And most of those sites haven’t been updated in ages. It’s no wonder; editing HTML or maintaining CMS takes considerable work and requires keeping up to date with the technologies involved. We just can’t realistically …