nnet2sas() supports centering and scaling

nnet2sas() version 1 introduced a way to export a nnet() model trained in R to Base SAS through metaprogramming, and now nnet2sas() version 2 introduces support for variable centering and scaling as implemented in caret::train(). See the link for version 1 for more background on nnet2sas().

### prepare demonstration data
require(earth) # for etitantic data
mydata <- etitanic
mydata$survived <- as.factor(ifelse(etitanic$survived==1, 'T', 'F'))

### train the neural network
require(pROC) # caret requires pROC with the ROC metric

fit <- train(
    survived ~ ., 
    data = mydata, 
    tuneLength = 2, 
    method = "nnet", 
    preProcess = c('center', 'scale'), 
    metric = "ROC",
    trControl = trainControl(summaryFunction = twoClassSummary, classProbs = T)

### show information about the training and neural network


### metaprogram SAS code

# nnet2sas version 2 
nnet2sas <- function(fit)
    if(!inherits(fit, c('train','nnet')))
        stop('nnet2sas requires an object returned by train() or nnet()')
    if(inherits(fit, 'train'))
        if(!inherits(fit$finalModel, 'nnet'))
            stop('expecting train() was used with method="nnet"')
        if (any(!(fit$preProcess$methods %in% c('center','scale'))))
            stop('preprocessing support is limited to center and scale')
        nn <- fit$finalModel
        preprocess_methods <- fit$preProcess$methods
    } else {
        nn <- fit
        fit$preProcess$methods <- numeric(0)

    sas <- paste("/* neural network size", paste(nn$n, collapse='-'), "*/\n")
    sas <- paste(sas, '/* inputs: ', paste(nn$coefnames, collapse=' '), ' */\n', sep='')
    sas <- paste(sas, '/* this macro handles extreme values */\n')
    sas <- paste(sas, '%macro logistic(z);\n')
    sas <- paste(sas, '1/(1+exp(min(max(-(&z),-500),500)))\n')
    sas <- paste(sas, '%mend;\n')
    # Define the input layer.
    # If there are factors, then in SAS you will have to manually change
    # something like 'pclass2nd' to 'pclass eq "2nd"'.
    # Also, this is the place to apply a range transformation (if any).
    for (input in 1:nn$n[1]){
        inputvar <- inputvar.org <- nn$coefnames[input]
        if ('center' %in% fit$preProcess$method)
            inputvar <- paste('(',inputvar,'-',fit$preProcess$mean[[inputvar.org]],')')
        if ('scale' %in% fit$preProcess$method)
            inputvar <- paste(inputvar,'/',fit$preProcess$std[[inputvar.org]])
        sas <- paste(sas, 'i', input,' = ', inputvar,';\n',sep='')

    # notation:
    # zji refers to z^j_i where j is the layer and i is the unit
    # aji refers to a^j_i is the activation of g(z^j_i) where g is the sigmoid function
    # compute the hidden layer from the input layer
    for (h in 1:nn$n[2]) {
        unit.offset <- (nn$n[1]+1)*(h-1)+1
        z2 <- c()
        # bias unit (intercept)
        z2[1] <- paste('z2',h,' = ',nn$wts[unit.offset],sep='')
        # loop through input layer
        for (input in 1:nn$n[1]){
            z2[input+1] <- paste('(',nn$wts[unit.offset+input],' * i', input, ')', sep='')
        sas <- paste(sas, paste(z2, collapse='+'),';\n',sep='')
        sas <- paste(sas, 'a2',h," = %logistic(z2",h,");\n", sep='')
    # compute the output layer from the hidden layer
    output.offset <- (nn$n[1]+1)*(nn$n[2])
    # bias unit
    z3[1] <- paste('z31 = ',nn$wts[output.offset+1],sep='')
    # loop through the hidden layer
    for (h in 1:nn$n[2]) {
        z3[h+1] <- paste('(',nn$wts[output.offset + h + 1],' * a2', h, ')', sep='')
    sas <- paste(sas, paste(z3, collapse='+'),';\n',sep='')
    sas <- paste(sas, "o = %logistic(z31);\n", sep='')
    # clean up temporary SAS variables
    sas <- paste(sas,
        paste('drop ',paste('i', 1:nn$n[1], collapse=' ', sep=''), ' ',
        paste('z2', 1:nn$n[2], collapse=' ', sep=''),' ',
        paste('a2', 1:nn$n[2], collapse=' ', sep=''),
        ' z31 ;\n', sep=''))
# This is how to invoke the metaprogramming function with
# the fitted neural network as the input.
sascode <- nnet2sas(fit)
# Print SAS code to the R console.  In this case, you need something
# like NotePad++ to replace the \n line break with a real line break.
# Then you can paste it into SAS.

# Export the predictors and predictions, so we can verify accuracy in Base SAS.
mydata <- cbind(mydata, predict(fit, etitanic, type="prob"))
write.csv(mydata, "etitanic.csv", row.names=F, quote=F)

Update: This function and similar functions are now in the mlmeta package, a package for metaprogramming between R and SAS.


2 thoughts on “nnet2sas() supports centering and scaling

  1. Hi Andrew, Thanks for this! To get more neurons for the hidden layer would we just change tunelength or modify createGrid in caret package? Thank you, Dan

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