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Update: The R2 function is deprecated. You can get R2 by the postResample function now. The code is here and shows in line 136 and 142 the formula: resamplCor <- try(cor(pred, obs, use = "pairwise.complete.obs"), silent = TRUE ... out <- c(sqrt(mse), resamplCor^2, mae) So postResample uses the squared correlation to calculate R2.


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Best case you predefine your indices via createMultiFolds. Its important that by default - if "cv" selected instead of "repeatedcv" or repeates not defined in trainControl - there won't be repeates. So, you have to predefine you multifold indices then set the number of repeates in the trainControl. k - number of the folds will be automatically recognized ...


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