I have a little question concerning the ‘tune’ function.
Indeed, in sPLS Liver Toxicity Case Study | mixOmics, it is written that for PLS2, we should use ‘cor’ instead of ‘MAE’ measure. By doing this and plotting the result, I get this picture.
However, by asking tune.spls$choice.keepX, I get
Hence, it seems choice.keepX minimizes the measure. Shouldn’t we maximize it instead, as we want the highest correlation between predicted and actual components?