parksw3 / mumps

Modeling the population-level impact of a third dose of MMR vaccine on a mumps outbreak at the University of Iowa

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This repository contains all code used for the analysis.

• R: contains R scripts for combining axes (for plotting) and simulating the main model
• analysis_seirv_final: contains R scripts for exclusion/inclusion analyses and vaccine scenario simulations
• doc: contains latex files for the manuscript
• figure: contains R scripts for plotting model diagram (Figure S1) and time series (Figure 1)
• figure_stanfit_seirv_final: contains all other figures presented in the paper
  • figure_stanfit_Rt_comp.R: R script for estimating Rt using the Wallinga-Teunis approach and plotting (Figure S3)
  • figure_stanfit_effects.R: R script for summarizing and plotting the results of exclusion and inclusion analyses (Figure 3, S7)
  • figure_stanfit_param_all.R: R script for plotting posterior distributions for the main model for different delays between vaccination and protection (Figure S4)
  • figure_stanfit_param_avg.R: R script for plotting posterior distributions for the model that assumes a single holiday effect term (Figure S5)
  • figure_stanfit_strategy.R: R scripts for plotting vaccine strategy simulations (Figure 4, S8)
  • figure_stanfit_total.R: R script for plotting the total number of cases among second and third dose recipients (Figure S2)
  • figure_stanfit_trajectory.R: R script for plotting the model fit (Figure 2)
• pomp: contains R scripts for evaluating the likelihood using the stochastic model
  • pomp_model.R: R script for setting up the POMP model
  • pomp_loglik.R: R script for evaluating the likelihood using the stochastic model
  • figure_pomp_loglik.R: R script for calculating the profile likelihood and plotting
• stanfit: contains R scripts for fitting deterministic models using rstan
  • stanfit_seirv_final.R: fitting deterministic models assuming a 7-day protection between vaccination and protection
  • stanfit_seirv_final_14.R: fitting deterministic models assuming a 14-day protection between vaccination and protection
  • stanfit_seirv_final_21.R: fitting deterministic models assuming a 21-day protection between vaccination and protection
  • stanfit_seirv_avg.R: fitting deterministic models assuming a single holiday effect
• stanmodel: constrains stan scripts for deterministic models
  • seirv_final.R: stan script for the main model
  • seirv_avg.R: stan script for the supplementary model that assumes a single holiday effect