Code for a study assessing the impact and cost-effectiveness of maternal vaccination and long-acting monoclonal antibodies against RSV in England and Wales
This Github repository contains code to produce the figures in our paper "" on medRxiv. The code heavily depends on a package which runs the simulations and cost-effectiveness for user-defined parameters, rsvie.
First install R.
Though this repository is set up like an R package, I recommend you clone this package from GitHub and work through the vignettes.
The code depends on several packages on CRAN, which should install automatically by running the R/main.R script via the pacman package. Another package on this Github account runs the RSV model, rsvie, which also needs to be installed. This can be done by installing the devtools packages and calling
library(devtools)
github_install("dchodge/rsvie")
library(rsvie)
The information in data/, data-raw/, and datasource/ relate to the England and Wales-specific information parameterising the burden, risk of outcomes, costs and QALY loss. For more details on how this works, please see the rsvie package.
The figs/ folder contains all the figures in the manuscript and supplementary.
The outputs/ folder contains large RDS files that contain all the information about the impact and cost-effectiveness of each model after running the simulations via the 'rsvie`; package.
The R/ folder contains all the code used to run the models, process the outputs and plot the figures.
The run_figs.Rmd vignette recreates all the figures and supplementary figures in the manuscript.
The get_metrics.Rmd vignette recreates the values quoted in the manuscript's results section.
The rshiny.Rmd vignette creates a local RShiny app, which allows the user to explore the impact on the cost-effectiveness analysis when changing coverage and combined cost of purchasing and administration per dose of long-acting monoclonals and maternal vaccination.
Any questions, please email me on david.hodgson@lshtm.ac.uk