I should have actually created some test code for you. Here is an example:
library(neuralnet) data(infert) # create your formula fm <- as.formula(paste("case ~ ", paste(colnames(infert)[c(3,4,6)], collapse="+"))) # call neuralnet net.infert <- neuralnet(fm, infert, err.fct="ce", linear.output=FALSE, likelihood=TRUE) You don't want to index your dataset like that, you should utilize the formula interface. Interestingly, the '.' notation doesn't seem to work here. Your formula call probably will look like this: fm <- as.formula(paste("resp ~ ", paste(colnames(data), collapse="+"))) And you call would be out1 <- neuralnet(fm,data=mydata, hidden = 4, lifesign = "minimal", linear.output = FALSE, threshold = 0.1) Regards, Charles On Tue, Mar 24, 2015 at 9:56 AM, Soheila Khodakarim <lkhodaka...@gmail.com> wrote: > Dear Charles, > > Thanks for your guide. > I run this code: > > library("neuralnet") > resp<-c(1,1,1,0,1,0,1,0,1,0,1,0,1,0,1,1,0,1,0,1) > mydata <- cbind(data, resp) > out1 <- neuralnet(resp~mydata[,1:3110],data=mydata, hidden = 4, lifesign = > "minimal", linear.output = FALSE, threshold = 0.1) > > I saw this error > > Error in neurons[[i]] %*% weights[[i]] : non-conformable arguments > > :(:(:( > > What should I do now?? > > Regards, > Soheila > > > On Tue, Mar 24, 2015 at 3:48 PM, Charles Determan Jr <deter...@umn.edu> > wrote: > >> Hi Soheila, >> >> You are using the formula argument incorrectly. The neuralnet function >> has a separate argument for data aptly names 'data'. You can review the >> arguments by looking at the documentation with ?neuralnet. >> >> As I cannot reproduce your data the following is not tested but I think >> should work for you. >> >> # Join your response variable to your data set. >> mydata <- cbind(data, resp) >> >> # Run neuralnet >> out <- neuralnet(resp ~ ., data=mydata, hidden = 4, lifesign = "minimal", >> linear.output = FALSE, threshold = 0.1,na.rm = >> TRUE) >> >> >> Best, >> Charles >> >> On Tue, Mar 24, 2015 at 4:47 AM, Soheila Khodakarim < >> lkhodaka...@gmail.com> wrote: >> >>> Dear All, >>> >>> I want to run "neural network" on my dataset. >>> ########################################################## >>> resp<-c(1,1,1,0,1,0,1,0,1,0,1,0,1,0,1,1,0,1,0,1) >>> dim(data) >>> #20*3110 >>> >>> out <- neuralnet(y ~ data, hidden = 4, lifesign = "minimal", >>> linear.output >>> = FALSE, threshold = 0.1,na.rm = TRUE) >>> ################################################################ >>> but I see this Error >>> Error in varify.variables(data, formula, startweights, >>> learningrate.limit, >>> : >>> argument "data" is missing, with no default >>> >>> What should I do now?? >>> >>> Best Regards, >>> Soheila >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> 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. >>> >> >> >> >> >> > -- Dr. Charles Determan, PhD Integrated Biosciences [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.