2. The ocvImpact package

Overview

Our own ocvImpact package is designed to help us run the model that estimates the impact of oral cholera vaccination campaigns using model inputs and outputs from the Vaccine Impact Modeling Consortium (VIMC).

The whole package can be found under gavi_vimc_cholera/packages/ocvImpact/ directory using this link.

The scripts to utilize this R package is under gavi_vimc_cholera/scripts/ directory using this link.

How to install this package

This package can be installed automatically by running the scripts as long as all the setup steps are completed. However, if you want to install it without having to run the whole simulation, we could try the following code:

   if (!require('ocvImpact', character.only = T)) {
   roxygen2::roxygenise("packages/ocvImpact")
   install.packages("packages/ocvImpact", type = "source", repos = NULL)
   library('ocvImpact', character.only = T)}

Sometimes you may need to first install devtools package and Rtools or Rtools40 package depending on which version of R you are using. Usually, you can complete this step by just following the prompts. However, if you encounter issues with installing Rtools40 package for your 4.0-or-above R, you could try out the following code:

   writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
   Sys.which("make")
   install.packages("jsonlite", type = "source")
   install.packages('rtools40', type = "source")

This solution is provided originally here.