gizembilgin/SLE_maternalPneumococcal_model

Code associated with "Modelling the impact of maternal pneumococcal vaccination on infant pneumococcal disease in low-income settings" [published in Vaccine] & "Cost-effectiveness analysis of a maternal pneumococcal vaccine in low-income, high-burden settings such as Sierra Leone" [published in PLOS GPH] # SLE_maternalPneumococcal_model **Associated paper(s):** * Modelling the impact of maternal pneumococcal vaccination on infant pneumococcal disease in low-income settings - published in Vaccine, see doi.org * Cost-effectiveness analysis of a maternal pneumococcal vaccine in low-income, high-burden settings such as Sierra Leone - published in PLOS Global Public Health, see doi.org ## Project overview Maternal pneumococcal vaccines have been proposed as a strategy for protection in early childhood before direct immunity through infant pneumococcal conjugate vaccines develop. To our knowledge, this project offers the most comprehensive estimates of the impacts of a maternal pneumococcal vaccine. We developed a mathematical model informed by previous small-scale studies of maternal pneumococcal vaccination, and the characteristics of existing maternal tetanus, pertussis and influenza vaccines. We then used these expected characteristics of a maternal pneumoccocal vaccine to undertake cost-effectiveness analysis informed by previous studies of pneumococcal conjugate vaccines. ## Code history The underlying transmission model was initially developed in 2019 in MATLAB as part of GMB's Honour Thesis. The scripts were later translated into Python and then R as part of the publication process of the mathematical modelling paper in 2021; version control history is available from this point. The cost-effectiveness analysis components were developed in 2021. ## Scripts included in this project * *1_inputs/* contains all parameter files * *x_results/* contains results * ***(0)_command_desk.R* runs all sub-scripts of the transmission model to complete one standard 'run'** * *(1-6)** scripts are the sub-scripts of the transmission model * ***(7)_cost_effectiveness_analysis* runs all sub-scripts of the cost-effectiveness analysis to complete one standard 'run'** * *(command)** scripts initiate complete ru …