[R] missing in neural network

[Charles Determan Jr]

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 <lkhodakarim at 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 <deter088 at 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 <
>> lkhodakarim at 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
>>>
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>>>
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>>
>>
>>
>>
>>
>


-- 
Dr. Charles Determan, PhD
Integrated Biosciences

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