The caret package for R provides a variety of error metrics for regression models and 2-class classification models, but only calculates Accuracy and Kappa for multi-class models. Therefore, I wrote the following function to allow caret:::train t...
Monthly Archives: July 2012
RSAP, Rook and ERP
As I wrote in my blog Analytics with SAP and R (Windows version) we can use RSAP to connect to our ERP system and play with the data. This time I wanted of course, to keep exploring the capabilities of RSAP, but using something else. As everybody kno...
Fix Overplotting with Colored Contour Lines
I saw this plot in the supplement of a recent paper comparing microarray results to RNA-seq results. Nothing earth-shattering in the paper - you've probably seen a similar comparison many times before - but I liked how they solved the overplotting...
Interest Differencing: Folk Commonly Followed by Tweeting MPs of Different Parties
Earlier this year I doodled a recipe for comparing the folk commonly followed by users of a couple of BBC programme hashtags (Social Media Interest Maps of Newsnight and BBCQT Twitterers). Prompted in part by a tweet from Michael Smethurst/@fantasticlife about generating an ESP map for UK politicians (something I’ve also doodled before – Sketching 
A practical introduction to garch modeling
We look at volatility clustering, and some aspects of modeling it with a univariate GARCH(1,1) model. Volatility clustering Volatility clustering — the phenomenon of there being periods of relative calm and periods of high volatility — is a seemingly universal attribute of market data. There is no universally accepted explanation of it. GARCH (Generalized AutoRegressive … Continue reading...
automated cell phenotyping — R package “EBImage”
Counting cells under microscope is always laborious and null. Those in the art would be relieved with assistance of a powerful image processing package, EBImage. Images are treated as “Image” objects, essentially multi-dimensional arrays. The class “Image” contains spatial information, pixel … Continue reading →
More Exploration of Crazy RUT
Unintentionally while playing with the lawstat package in R, I started trying to build systems (STANDARD DISCLAIMER: NOT INVESTMENT ADVICE AND WILL LOSE LOTS OF MONEY SO PROCEED WITH CAUTION) based on the Jarque Bera test of normality (entry in Wikiped...
A better ‘nls’ (?)
Those that do a lot of nonlinear regression will love the nls function of R. In most of the cases it works really well, but there are some mishaps that can occur when using bad starting values for the parameters. One of the most dreaded is the “singular gradient matrix at initial parameter estimates” which 
Health Care Costs – Part 1, "The Problem"
The Problem In the United States, health care costs have been going up for a number of years, even when adjusted for inflation. Not unlike a runaway freight train, this rampant inflation cannot continue indefinitely without crashing. ...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
