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Random forest imputation should be further investigated in situations where MICE with default parametric imputation models produces biased results.
This meant that there were no interactions in the substantive model, but the default parametric imputation model for x3 (which would not include any interactions) would be incorrect.
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In this paper, the default pair of non parametric statistics is used, which are the mean difference test and the Mann-Whitney U test.
If this can not be confirmed then it is proper to default to a non-parametric approach of which there are several [40], [62], [79].
The false discovery rate (FDR) corrections were as set by default 0.05 and 0.10 for the "parametric non-weighted" and the "non-parametric weighted" methods, respectively.
Comparisons of alpha diversity indices were achieved in R with the default statistical package (2.15.13; Vienna, Austria) using non-parametric Mann–Whitney or the Kruskal Wallis tests, followed by a multiple comparison test depending of the number of categories compared.
By default, SPM performs serial orthogonalization such that the first parametric regressor includes both shared variance and its unique variance, and the second parametric regressor includes only its unique variance.
The distribution of gene sets in ranked GWAS results was examined using the non-parametric algorithm in the GSEA tool, with default values for all parameters [31] except for the set size when appropriated.
All reasonable efforts were made to standardise each method towards a parametric parity, while staying as close to their defaults as possible.
Initial results for the semi-parametric penalized likelihood method were obtained with the default settings of r8s using cross-validation to find the smoothing parameter resulting in the lowest cross validation scores.
The FBF algorithm was implemented in MATLAB 7.7, using functions available within the Statistical Parametric Mapping (SPM8, http://www.fil.ion.ucl.ac.uk/spm/) with the default settings for the optimisation, interpolation, image smoothing and histogram smoothing.
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