Note: Almost all of my development is in MCMC algorithms right now.
OCTAVE VS MATLAB LICENSE
Further, as it's free you also don't have deal with the Godforsaken flexlm license manager. Lastly, the R community appears to be growing much faster and with much more momentum than the Matlab community ever had. Perhaps the newer versions work better, but I can think of two situations off the top of my head where a C++ dll in the back of Matlab caused Windows XP to blue screen because I walked inappropriately outside an array bounds - a very hard problem to debug if your computer reboots every time you make that mistake. Disclaimer: Being a grad student, I haven't used a recent version of Matlab for my dlls, I've been working almost exclusively in Matlab 7.1 (which is like 4 years old). I have experience wrapping C++ into both Matlab and R (and excel for that matter), but I've had a better experience with R. However, I find that if you want algorithms to function efficiently within a production environment, it is best to move to a compiled language like C++. I'm still learning it, but I'm starting to leave Matlab in the dust because once you know R, it's also fairly easy to prototype functions there.
I often prototype functions & algorithms in Matlab because, as stated, it is easier to express an algorithm in something which is close to a pure mathematical language.
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