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The multiple imputation part of the procedure is handled by the R-package MICE (https://cran.r-project.org/web/packages/mice/index.html).html
Based on the results on the quality measures and regarding computation time (GATK which supports multiple threads was faster than SAMtools and freebayes, as shown in Additional file 8) and usefulness (i.e. quality, completeness and availability) of the software documentation, we decided to use the variants called by GATK as basis for the imputation part of this study.
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Our aim is to impute the missing values of Y : this may either be the whole imputation task, part of a monotone imputation procedure, or part of a MICE algorithm.
As data on BMI were missing in 25% of patients, we performed multiple imputation as part of a sensitivity analysis.
The CNSTAT report favored inverse probability weighted generalized estimating equation (GEE) methods and multiple imputation, in part because auxiliary data associated with missingness can be incorporated into the analysis [ 18].
In either case, random numbers are used in the multiple imputation model as part of the process of drawing parameter values from a predetermined set of options.
One of the reasons for this lack of consistency is the fact that there is a diversity of opinion about the use of the imputation on the part of 'survey experts'.
To avoid this problem, missing data imputation becomes an important part of analysing economic data.
Rasch model-based imputation was performed as part of the BIGSTEPS [ 25] calculation during the item calibration.
However, in order to include all available data, multiple imputation was undertaken as part of a sensitivity analysis.
The basic principle is described by Rubin ([2003]): A few imputations of the first part are created (say M), and then for each of these, several imputations of the second part are created (say N).
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