diff --git a/ccn2019.rev3.Rmd b/ccn2019.rev3.Rmd index 223277f..5266c90 100644 --- a/ccn2019.rev3.Rmd +++ b/ccn2019.rev3.Rmd @@ -79,49 +79,66 @@ train_data <- data[1:split,] test_data <- data[(split+1):nrow(data),] -new_model <- train( +plsTrControl <- trainControl( + method = "cv", + number = 5 + ) + +# Train PLS model (accuracy+) +model_pls_rt <- train( + a ~ .-rt-al-correct, + data = train_data, + method = "pls", + tuneLength = 20, + trControl = plsTrControl, + preProc = c("zv","center","scale")) + +# Check CV profile +plot(model_pls_rt) + + + +# training control params for "correct" column +trControl <- trainControl( + method = "cv", + number = 5, + classProbs = T, + summaryFunction = twoClassSummary + ) + +model_glm_correct <- train( correct ~ .-rt-a-al, data = train_data, method = "glm", family = "binomial", - trControl = trainControl( - method = "cv", - number = 5, - classProbs = T, - summaryFunction = twoClassSummary - ) + trControl = trControl ) -new_model +model_glm_correct -predicted_new_data <- predict(new_model, test_data, type="prob") +predicted_correct_data <- predict(model_glm_correct, test_data, type="prob") -confusionMatrix(test_data$correct, predicted_new_data) +confusionMatrix(test_data$correct, predicted_correct_data) library(caTools) -colAUC(predicted_new_data, test_data$correct, plotROC=T) +colAUC(predicted_correct_data, test_data$correct, plotROC=T) ## OLD MODEL (only global features) -old_model <- train( +model_glm_correct_old <- train( correct ~ n+t+v, data = train_data, method = "glm", family = "binomial", - trControl = trainControl( - method = "cv", - number = 5, - classProbs = T, - summaryFunction = twoClassSummary - ) + trControl = trControl ) -old_model +model_glm_correct_old -predicted_old_data <- predict(old_model, test_data, type="prob") +predicted_old_correct_data <- predict(model_glm_correct_old, test_data, type="prob") -confusionMatrix(test_data$correct, predicted_old_data) +confusionMatrix(test_data$correct, predicted_old_correct_data) library(caTools) -colAUC(predicted_old_data,test_data$correct, plotROC=T) +colAUC(predicted_old_correct_data,test_data$correct, plotROC=T) ```