How to use lapply with get.confusion_matrix() in R?

Question

I am performing a PLS-DA analysis in R using the mixOmics package. I have one binary Y variable (presence or absence of wetland) and 21 continuous predictor variables (X) with values ranging from 1 to 100. I have made the model with the data_training dataset and want to predict new outcomes with the data_validation dataset. These datasets have exactly the same structure.

My code looks like:

library(mixOmics)
model.plsda<-plsda(X,Y, ncomp = 10)
myPredictions <- predict(model.plsda, newdata = data_validation[,-1], dist = "max.dist")

I want to predict the outcome based on 10, 9, 8, ... to 2 principal components. By using the get.confusion_matrix function, I want to estimate the error rate for every number of principal components.

prediction <- myPredictions$class$max.dist[,10] #prediction based on 10 components
confusion.mat = get.confusion_matrix(truth = data_validatie[,1], predicted = prediction)
get.BER(confusion.mat)

I can do this seperately for 10 times, but I want do that a little faster. Therefore I was thinking of making a list with the results of prediction for every number of components...

library(BBmisc)
prediction_test <- myPredictions$class$max.dist
predictions_components <- convertColsToList(prediction_test, name.list = T, name.vector = T, factors.as.char = T)

...and then using lapply with the get.confusion_matrix and get.BER function. But then I don't know how to do that. I have searched on the internet, but I can't find a solution that works. How can I do this?

Many thanks for your help!

dcarlson · Accepted Answer · 2020-12-24T04:58:43.650

Without reproducible there is no way to test this but you need to convert the code you want to run each time into a function. Something like this:

confmat <- function(x) {
        prediction <- myPredictions$class$max.dist[,x] #prediction based on 10 components
        confusion.mat = get.confusion_matrix(truth = data_validatie[,1], predicted = prediction)
        get.BER(confusion.mat)  
}

Now lapply:

results <- lapply(10:2, confmat)

That will return a list with the get.BER results for each number of PCs so results[[1]] will be the results for 10 PCs. You will not get values for prediction or confusionmat unless they are included in the results returned by get.BER. If you want all of that, you need to replace the last line to the function with return(list(prediction, confusionmat, get.BER(confusion.mat)). This will produce a list of the lists so that results[[1]][[1]] will be the results of prediction for 10 PCs and results[[1]][[2]] and results[[1]][[3]] will be confusionmat and get.BER(confusion.mat) respectively.

How to use lapply with get.confusion_matrix() in R?

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