Extended Data Fig. 6: Validation of the incidence rate and transmission flow models.

(a) Empirical HIV incidence rates were obtained for each of the 50 data sets with imputed exposure times and compared to the estimated HIV incidence rates under the Poisson model. The median (point) and 95% range (horizontal error bars) of the crude HIV incidence rates are plotted against the posterior median (point) and 95% range (vertical error bars) of estimated HIV incidence rates for each gender, age and round. (b) Prior incidence rates as specified according to the outputs of the incidence rate and used in the transmission model are compared versus the posterior incidence rates obtained with the transmission model. Shown are medians (point) and 95% credible intervals (error bars) by gender, age and round. (c) Observed transmission flow counts are compared to posterior predictive estimates under the transmission model. Shown are medians (point) and 95% credible intervals (error bars) by direction of transmission, time period, and age of the phylogenetically likely source. Throughout all subfigures, empirical and modelled incidence estimates are based on n = 1,117 individuals in the incidence cohort and n = 227 source–recipient pairs among n = 1,978 individuals in the transmission cohort.