Codes for pertussis serotransmission model

This folder contains R and C codes to reproduce the results described in the study, "Immune boosting and the perils of interpreting pertussis seroprevalence studies."

Required packages

The model was developed using the package "pomp" (version 5.10) in R version 4.4.1. Other required packages are listed in the script "s-base_packages.R"

Main scripts

• The model is created via a call to the function "f-CreateSerotransModel.R", which internally calls the C file "c-serotransmission_model.c"
• An example model simulation can be run using the script "m-check_model.R"
• The clustering of next-generation matrices (NGMs) is performed via the script "m-analyze_SCMs.R"
• The parameter estimation in six European countries is done via the script "m-run_simulations_empirical_comparison.R"
• The model predictions in twelve countries are run using the script "m-run_simulations.R"
• All other scripts are either auxiliary functions (prefix f-), support scripts (prefix s-), or scripts to make the figures

Data sources

• Social contact matrix (SCM) and demographic data:
  • Mistry et al., 2021
  • Associated online repository: https://github.com/mobs-lab/mixing-patterns
• Seroprevalence data:
  • Pebody et al., 2005 (Appendix table)
  • Wehlin et al., 2021 (Table 3)