mrajeev08/MadaAccess

Estimating access to human rabies vaccine in Madagascar # Access to PEP in Madagascar This repository accompanies the manuscript: *Rajeev, M. et al. How access to care shapes disease burden: the current impact of post-exposure prophylaxis and potential for expanded access to prevent human rabies deaths in Madagascar*. medrxiv preprint here Code to reproduce the analyses and figures are in analysis/src. The Rmarkdown document and associated supporting files to reproduce the manuscript are in analysis/paper. ## Reproducing results All analyses were completed in R version 4.0.2. All rmarkdown outputs require `rmarkdown`. ### Step 1: Clone the repository & also download intermediate outputs from zenodo. ``` git clone github.com ``` Also, download the outputs from this zenodo link(also includes some of the raw data used in the analysis, although not all due to sharing restrictions). ### Step 2: Install dependencies - Option 1: using `renv` (will install version specific to renv & local package library) In R or Rstudio run this command: ``` renv::restore() ``` This will throw a warning if you're using a different R version from 4.0.2 used for this analysis. - Option 2: Source the script analysis/src/00_install.R (will install most recent to global package library). **You will also need to download and install JAGS.** ### Step 3: Run the analysis The scripts are numbered sequentially according to how the should be run. If you're in a unix environment, you can use the bash script runit.sh to run all analysis steps sequentially by: ``` ./runit.sh -d "analysis/src/*/*" --printErrors -q ``` or to just make the figures: ``` ./runit.sh -d "analysis/src/figures/*" --printErrors -q ``` To run the steps which were completed on a cluster, you will need to pass the `-cl` argument: ``` ./runit.sh -d "analysis/src/*/*" --printErrors -q -cl ``` and then enter 1 to run the scripts in parallel or 2 to run serially on your local computer. The easiest way to make the paper is in it's html for …