I have some doubts about which performance measure to use, area under the ROC curve (TPR as a function of FPR) or area under the precision-recall curve (precision as a function of recall).
My data is imbalanced, i.e., the number of negative instances is much larger than positive instances.
I am using the output prediction of weka, a sample is:
inst#,actual,predicted,prediction 1,2:0,2:0,0.873 2,2:0,2:0,0.972 3,2:0,2:0,0.97 4,2:0,2:0,0.97 5,2:0,2:0,0.97 6,2:0,2:0,0.896 7,2:0,2:0,0.973
And I am using pROC and ROCR r libraries.