recalculateSVMparams: Calculate SVM hyperparameters based on grid search

In ddgraph: Distinguish direct and indirect interactions with Graphical Modelling

Description

Find the cost/gamma parameters based on a grid search by best AUC and by limiting the number of support vectors. Currently only supports discreet binary data.

Usage

recalculateSVMparams(cost.range, gamma.range, d,
    class.weight=1/table(convertToFactor(d$class)), kernel="radial",
    max.prop.SV=0.9)

Arguments

cost.range	the range of cost parameter values to evaluate
gamma.range	the range of gamma parameter values to evaluate
d	the data.frame with variables as columns, the class labels must be labelled with "class"
class.weight	the class weights to use (if there is an large bias for positive/negative class)
kernel	kernel type to use (takes valid package e1071 names like "radial")
max.prop.SV	the maximal proportion of support vectors to number of data points (rows in d)

Value

a list with the two parameters that give best AUC in LOOCV

Examples

## Not run: 
data(mesoBin)
# get SVM AUC etc over cost rage of 1, 100, and gamma range of 0.1, 1
recalculateSVMparams(c(1, 100), c(0.1, 1), convertToFactor(rawData(mesoBin$Meso)))

## End(Not run)

ddgraph documentation built on Nov. 17, 2017, 10:50 a.m.