I'm doing nested resampling with a 4x3 setup (4-fold cross-validation in the outer loop, and 3-fold cross-validation in the inner loop). For now, I only use Support Vector Machines (ksvm from kernlab). In the inner loop, I'm looking for the optimal tuning parameters C and sigma.
Calling getBMRPerformances() then outputs me the performances on the 4 individual outer test data sets. The function getBMRTuneResults() outputs 4 values for the measure I am using (in my case cohen's kappa) as well but they differ from the output of getBMRPerformances() and I don't understand what the second output actually is.