Distribution of unadjusted and bootstrap-adjusted estimators of group-wise linkage probabilities, using proportionate subsampling for a 70% sample of Mochudi data.

<p>Distribution of unadjusted and bootstrap-adjusted estimators of group-wise linkage probabilities, using proportionate subsampling for a 70% sample of Mochudi data.</p

Estimated probability of linkage between individuals of different groups, , from Mochudi data.

<p>Rates given are per 1000 pairs. A link in this analysis is defined by a difference between sequences in less than 10% of available sites.</p

Schematic of the sequence-imputation method.

<p>Schematic of the sequence-imputation method.</p

Point estimates and 95% confidence intervals for unadjusted and bootstrap-adjusted estimates of groupwise linkage rates in Mochudi.

<p>The distance cutoff defining linkage between sequences ranges from 0.085 to 0.12.</p

Estimates of conditional probability of linkage by groups, , for a 70% sample of the full Mochudi data.

<p>Red line represents the “truth” as observed in the full data.</p

Estimating the true proportion of clustering in the Mochudi population.

<p>Treating the observed Mochudi data (N = 371) as a biased sample from the population, and imputing the imputed-population dataset (N = 504) based on Botswana and Mochudi-specific age and gender breakdowns to create a database with the same demographic structure as Botswana as a whole. Point estimates and error bars for the 0.10 and 0.15 thresholds of clustering.</p

Diagnostic plots of subsample correlations by group, .

<p>Diagnostic plots of subsample correlations by group, .</p

Average relative bias of adjusted (red) and unadjusted (black) estimators of group-wise linkage rates over general time-reversible evolutionary model simulations.

<p>Average relative bias of adjusted (red) and unadjusted (black) estimators of group-wise linkage rates over general time-reversible evolutionary model simulations.</p

Estimates of conditional probability of linkage by groups, , for the full Mochudi data.

<p>Estimates of conditional probability of linkage by groups, , for the full Mochudi data.</p

Estimated overall proportion of clustering for observed, incomplete-observed and imputed-complete datasets under MNAR.

<p>Clustering assessed at the 0.10 threshold, with <i>m</i> = 100 deletions. <i>Clus</i> stands for clustering; <i>Obs</i> for observed data; <i>In-Obs</i> for ncomplete-observed data; <i>Impute-Com</i> for imputed-complete data; <i>Cov</i> stands for coverage.</p><p>Estimated overall proportion of clustering for observed, incomplete-observed and imputed-complete datasets under MNAR.</p