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(D) Observed and predicted training set error rate distributions for Model logP3-1b.
Table 2 Results with different combinations of training set validation set in study site Chitwan Training set Error stat.
Table 1 Results with different combinations of training set validation set in study site Gorkha Training set Error stat.
In RF method, there is no need for cross-validation or a separate test set to get an unbiased estimate of the test set error [37].
(D) Calculated uncertainty profiles and distributions of observed validation set error rates for model CYP2D6-1a (naïvotinging threshold at 16.5; red), and errors for model CYP2D6-1b (refined threshold at 27.5; green).
(A) The validation set error distribution for logP3-2a (for which the naïve threshold of 37.5 was used) is shown in red and the error distribution for logP3-2b (refined voting threshold: 53.5) is shown in green.
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The performance reported here is based on test set errors.
This second set of parameters provided on average smaller training and validation set errors and calculated models with the smaller number of support vectors.
Therefore, we set errors of vertical displacements (eh i ) to be three times of uncertainty of change in baseline length (i.e., eh i = 3ex i = 3ey i ).
Because these OOB samples have not been used in the tree construction, they can be used to estimate test set errors (OOB error).
We set the error tolerance for all algorithms as ε=10−4.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com