Estimating the impact of introducing PCV13/15/20 or PPV23 in the over-55 populations of England, Brazil, Malawi and South Africa.
Code by Deus Thindwa and Sam Clifford under the supervision of Stefan Flasche and in collaboration with researchers from National Laboratory for Meningitis and Pneumococcal Infections, Adolfo Lutz in Brazil, UK Health Security Agency in England, Malawi Liverpool Wellcome Programme in Malawi and National Institute for Communicale Diseases in South Africa.
The data stored in /data are loaded and analysed by the code in /script, with resulting figures and tables created in /output.
Briefly, the code fits an exponential increase in incidence of Streptococcus pneumoniae by age for each data set and simulates predicted incidences. These are then combined with age-fractionated population data and estimates of vaccine efficacy by time since vaccination (with optional age-dependence) to obtain estimates of the number of averted cases given the vaccine programme (both per vaccinee within the population).