Code for the manuscript: Impact of pneumococcal conjugate vaccines on invasive pneumococcal disease-causing lineages among South African children

Code 1 (lineage IRRs.R): Lineage incidence rate ratio calculation

Code 2 (amr_glm.R): AMR linear regression analysis

Scripts are derived from the original repo https://github.com/rgladstone/GPSCs/tree/master/lo_et_al