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There are various likely sources of extra-variation in the estimated risk difference.
Statistical significance of the extra variation accounted for by the presence of the haplotype groups in the model was determined using approximate F-statistics derived from Wald statistics with denominator degrees of freedom estimated in the Genstat REML procedure [ 25].
We checked for overdispersion by fitting negative binomial regression models and assessing the significance of the extra variation parameter.
The objective of this paper is to examine and correct for the influence of both sources of variation, i.e., variation induced by sampling as well as extra variation created by incomplete data.
However, the extent of this advantage decreases as minor allele frequency increases due to the tradeoff between EM-SNP's bias adjustment for the estimation of minor allele frequencies and extra variation introduced in the EM algorithm.
We found that using haplotypes in addition to SNP genotypes in the analysis accounted for no extra variation for any of the SNP/trait combinations.
The evaluation of extra binomial variation was performed using the PQL estimation.
We found no evidence of extra binomial variation using a chi-square test in an empty model without any covariates or poverty rate, suggesting that the logistic model was appropriate.
For 10% of the filler items, this was not the case to bring in some extra variation.
However, geostatistical analysis shows that the extra variation is not substantial, and there was no need for redesign of the irrigation valve areas.
Extra variation is allowed in the model for these values by inclusion of an additional random effect.
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