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Where numbers do not sum to column total this is due to missing data, percentages are presented for non-missing data.
Prior to analysis, the dataset was analyzed for missing data (see Table 1 for variable level missing data percentages).
Table 1 describes the baseline characteristics of the cohort, including summary statistics and missing data percentages for all explanatory variables where complete data were not observed.
All analyses were conducted using SPSS version 22.> -wrap-foot> N's may not sum to total due to missing data; percentages reported are percent of valid data.
For the full 206 accessions by 253 markers dataset, the missing data percentages ranged from 0 to 6.3 % (mean 1.7%%) between accessions and 0 to 11.7 % (mean 1.7%%) between markers.
Note: Valid cases = those with no missing data Percentages are reported for rows Multivariate logistic regression is shown in Table 5 for complete cases i.e. a complete case analysis with the entered variables defining a complete case.
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The missing data percentage is 13.4percentt for the whole sample: 11.8 percent for developed countries and 13.9percentt for developing countries.
Sub-Saharan Africa has a missing data percentage of 13.7 percent, South Asia has no missing data, and the rest of the world has 14.1percentt missing.
Filtering SNPs based on missing data percentage had little to no effect on prediction accuracy, especially when random forest imputation was used to impute missing values.
LIFDCs have a missing data percentage of 12.4percentt (and the rest of the world has 14.4 percent), and LDCs have 24.2percentt (and the rest of the world has 9.7percentt).
For every different combination of missing data percentage and noise level, a dataset was generated by homogeneously distributing missing data among columns of Y, the indices for each column being chosen at random.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com