In sbfnk/measles.katanga: Code accompanying the manuscript "The impact of reactive mass vaccination campaigns on measles outbreaks in the Katanga region, Democratic Republic of Congo" (doi:10.1101/201574).

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
# Please put your title here to include it in the file below.
Title <- "The impact of reactive mass vaccination campaigns on measles outbreaks in the Katanga region, Democratic Republic of Congo"

measles.katanga

This repository contains the data and code for our paper:

Sebastian Funk, Saki Takahashi, Joel Hellewell, Kartini Gadroen, Isidro Carrion-Martin, Marit van Lenthe, Katiana Rivette, Sebastian Dietrich, W. John Edmunds, M. Ruby Siddiqui and V. Bhargavi Rao (2019). r Title. medRxiv 19003434 https://doi.org/10.1101/19003434

How to download or install

You can download the compendium as a zip from from this URL: https://github.com/sbfnk/measles.katanga/archive/master.zip

Or you can install this compendium as an R package, measles.katanga, from GitHub with:

# install.packages("remotes")
remotes::install_github("sbfnk/measles.katanga")

Figures and analysis

Figures 1-4 can be re-created using

figure1()
figure2()
figure3()
figure4()

Figure 5 uses the outputs from the prediction model, which can be run using

p <- prediction_model()
figure5(p)

Figure 6 uses the outputs from the dynamic model. These are included in the model as libbi objects which can be retrieved using.

posterior <- rbi::read_libbi(system.file(package="measles.katanga", file.path("bi", "posterior.rds")))
posterior_no_mvc <- rbi::read_libbi(system.file(package="measles.katanga", file.path("bi", "posterior_no_mvc.rds")))

The two variables posterior and posterior_no_mvc then contain results from posterior sampling and using these to resimulate without mass vaccination campaigns, respectively. These can be re-created using

model <- posterior$model
posterior <- fit_dynamic_model(model, nbdata=10)
posterior_no_mvc <- remove_mvc(posterior)

The fit_dynamic_model command may take a few hours to run, depending on the hardware available (especially subject to availability of a fast Graphical Processing Unit, GPU).

From these two variables, Figure 6 can be re-created using

figure6(posterior, posterior_no_mvc)

sbfnk/measles.katanga documentation built on Nov. 11, 2019, 4:27 a.m.