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To limit the risk of contamination between clusters we used census data from Statistics South Africa to demarcate clusters with similar estimated population sizes and suitable borders or natural boundaries (such as roads, rivers, and hills).
As similarity measure between individual objects (diseases/TFs) we used the Euclidean distance, and for distance between clusters we used the average (Euclidean) distance between all pairs of objects.
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In order to distinguish quantitatively between mergers of different sized clusters, we used the FMI as a measure of similarity between the different clustering before and after each merger.
To determine significance of the difference between means of each group of clusters we used a two-tailed t-test.
To determine significance of the difference between medians of each group of clusters we used a one-tailed Mann-Whitney test.
As a metric for the hierarchical clustering we used the correlation between the parameter vectors (normalized inner product), and used average linkage as the method for hierarchical agglomeration of clusters.
For clustering, we used Pearson correlation as the distance measure and defined similarity between clusters using average-linkage clustering.
For gene-wise clustering, we used Pearson correlation coefficient as the distance measure and defined similarity between clusters using average-linkage clustering.
Given that some choice disability factors like partner violence are clustered, and there was a high degree of heterogeneity between clusters, we repeated the analysis using generalised estimating equation (GEE) in the R package Zelig [ 45] in an exchangeable correlation structure (logit.gee model, 1000 simulations, robust 95%CI).
To compare study outcomes between arms, we used cluster-specific method because households rather than patients were randomized.
To compare these parameters between all 3 different clusters of interneurons, we used a non-parametric ANOVA (Kruskal Wallis) test with Dunn's post-test analysis.
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