Here is what the train() function in the caret package does by default (you can change this behavior; see below).
Using the entire data set, estimate the RBF parameter using the sigest() function in the kernlab package (which, if I recall correctly involves the median of a sample of kernel matrix values). Using this fixed value, the cost function is varied over a common set of held-out samples. More specifically, every value of the cost parameter is evaluated on the same exact folds. I've been able to achieve pretty good performance this way in almost every case where I've done the comparison, Based on these performance values, you can select the cost function based on the best performance. There are also ways of selecting the simplest model that is within the uncertainty of the numerically optimal model (that is done using the selectionFunction argument of trainControl). I should also note that you can tune across any grid of cost and sigma (this is done via the tuneGrid argument of train()). Max ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
