Fig. 1: Fitting the model to testing and secondary school absences data.

The stochastic individual-based model is fitted to (a) the percentage of 11–16 year olds who test PCR positive (excluding confirmatory PCR tests) each day from 1st September 2020 to 23rd May 2021, (b) the percentage of 11–16 year olds who test LFT positive each day from 8th March 2021 to 23rd May 2021. Circles correspond to the data, with shaded intervals around mean model traces (solid lines) representing 95% prediction intervals in all plots. Shaded vertical grey regions represent time periods when schools were not fully open (either due to closures or school holidays). The model is also fitted to (c) the distribution of peak number of confirmed COVID-19 absences in secondary schools from 1st September 2020 to 18th December 2020, and (d) the distribution of peak number of confirmed COVID-19 absences in secondary schools from 8th March 2021 to 23rd May 2021. Circles denote the data and shaded blocks the 95% prediction interval estimated from the model. The plots above show the mean values obtained from 100 simulations in 2979 secondary schools, each with a distinct parameter set sampled from the posterior distribution.