The chemical similarity network or CSN is a great tool for organizing biological data based on known biochemistry or chemical structural similarity. Here is an example CSN for visualizing metabolomic changes (measured via GC/TOF) due to anaerobic stress in germinating seeds. In this network edges are formed for chemical similarity scores > 75. Node color describes 
Here are links to all of this year's posts (excluding seminar/webinar announcements), with the most visited posts in bold italic. As always, you can follow me on Twitter for more frequent updates. Happy new year!New Year's Resolution: Learn How to Code...
The forward (explicit) Euler method is a first-order numerical procedure for solving ODEs with a given initial value. The forward Euler method is said to be the simplest and most obvious numerical ODEs integrator. In fact, the simulation using the forward Euler only … Continue reading →
So as I sink deeper into the second level of R enlightenment, one thing troubled me. “lapply” is fine for looping over a single vector of elements, but it doesn’t do a nested loop structure. These tend to be pretty ubiquitous for me. I’m forever doing the same thing to a set of two or three 
This has been a great year for my blog. I've seen tremendous growth in my subscribers. I look forward to engaging with and learning from my followers in 2013 and I plan to offer valuable content in return. If you're interested in following along, you can quickly subscribe via RSS or e-mail. I use Google
I've been away for some time without closely following the media, and without significant internet access. When such a period is over it takes some time to regain momentum. Thus my short exit poll series will be continued in 2013. For now I'm still sor...
An earlier post looked at random shuffle for permutations. The STL also supports creation of random samples. Alas, it seems that this functionality has not been promoted to the C++ standard yet — so we will have to do with what is an extensions ...
Many of my software engineer friends ask me about learning data science. There are many articles on this subject from renowned data scientists (Dataspora, Gigaom, Quora, Hilary Mason). This post captures my journey (a software engin...
I’m being tortured by the mistakes of my past self. I think I’ve made most every mistake possible in creating a package and I want to go back in time and tell year ago me all I know now. But … Continue reading →
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
