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We repeated the model selection steps described above using first a pool of the parameters selected using the dry and wet season subsets and then a pool of the parameters selected with the rainfed field subset and the irrigated field subset.
After this step, the remaining SNPs are used for the dimensionality reduction and model selection steps of the MDR algorithm.
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Variable selection is a special case of a model selection step.
This heuristic avoids the model selection step and reduces the runtime of the preprocessing step.
In this model selection step, 3B makes many local decisions to incrementally adjust the model.
Therefore, a model selection step that determines an optimal number of components is necessary.
Hence, the model selection step has to be separated from the step of estimating the prediction error.
After a series of such decisions have been made, 3B re-optimizes the entire model (Step 2) and then repeats the model selection step (Step 3).
This model selection step involves a significant runtime overhead and can be avoided if the number of sub-distributions can be estimated.
Additionally, Bayesian data analysis, which provides a probabilistic framework for data analysis, is considered in detail, since it allows uncertainty quantification and validation of the model selection step.
Using new data ensures that the model assessment step is independent of the model selection step, which is necessary to be able to estimate the prediction error unbiasedly (see below).
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