I tried the following data(promotergene)
## train svm using custom kernel stringkernel<-stringdot(length = 4, lambda = 0.5, type = "sequence", normalized = TRUE) gene <- ksvm(Class~.,data=promotergene,kernel=stringkernel,C=10,cross=5) I get the following error cannot allocate vector of size 1.2 Gb. Is my usage wrong ?. I am running this under linux serve 6850 which has about 8Gb memory Any would be appreciated. Cheers../Murli ________________________________________ From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Nair, Murlidharan T [EMAIL PROTECTED] Sent: Wednesday, June 25, 2008 9:44 AM To: [EMAIL PROTECTED] Subject: [R] stringdot Hi!! I am trying to figure out how to use the string kernel "stringdot" in kernlab. k <- function(x,y) { (sum(x*y) +1)*exp(-0.001*sum((x-y)^2)) } class(k) <- "kernel" data(promotergene) ## train svm using custom kernel gene.k <- ksvm(Class~.,data=promotergene,kernel=k,C=10,cross=5) # works fine in this case gene.rbf <- ksvm(Class~.,data=promotergene,kernel="rbfdot",C=10,cross=5)# works fine with the rbf kernel gene.string <- ksvm(Class~.,data=promotergene,kernel="stringdot",C=10,cross=5) # this give the following error #Error in match.arg(kernel, c("rbfdot", "polydot", "tanhdot", "vanilladot", : # 'arg' should be one of “rbfdot”, “polydot”, “tanhdot”, “vanilladot”, “laplacedot”, “besseldot”, “anovadot”, “splinedot”, “matrix” What am I doing wrong here? Thanks ../Murli ______________________________________________ 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. ______________________________________________ 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.