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  "Title": "Estimate Transmission Assortativity Coefficients",
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  "Description": "Estimates group transmission assortativity coefficients\nfrom transmission trees. Group transmission assortativity\ncoefficients measure the tendency for individuals to transmit\nwithin their own group (e.g. age group, vaccination status, or\nlocation) compared to other groups. The package requires\ninformation on who infected whom, group membership for all\nindividuals, and the relative sizes of each group in the\npopulation. For more details see Geismar et al. (2024)\n<doi:10.1371/journal.pone.0313037>.",
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