markgdawson/covidm

Covidm library from LSHTM, provided as an R package

Covidm Package

This repository provides the backend for the LSHTM SEI3R model, found at this repository, as an R package. This is an early work in progress, please report any issues.

System Requirements

• The GNU GSL library (e.g. libgsl0-dev on Debian or Ubuntu)
• Rcpp

Installation

You will first need to install the devtools package with:

install.packages("devtools")

After that, you an install the covidm package with:

devtools::install_github("M4rkD/covidm")

Once the installation completes, you can load (and attach) the package with:

library(covidm)

Exported functions

Currently, only functions and data sets used by the UK.R script from the LSHTM covid-uk repository are export by this library, despite more functions being available internally. If you require more functions exported, please open an issue and I’ll be happy to export them. The intention of this approach is to only export functions which are useful.

UK.R Script

The UK.R script is included in the repository, but not the installed package, for reference. The changes necessary to use covidm as a package have been made to the UK.R script. Note however that the script has been modified to hardcode only a single iteration of a single analysis, for two days, for demonstration purposes only. Note in particular, the file for age varying symptomatic rate has been changed.

Running on Windows or Mac

Currently, this is not tested on Windows. If you still wish to go ahead, you should do so with gsl version 2.4.

If you’re interested in working on Windows, please raise an issue.

The Mac installation has not yet been tested, but hopefully will be tested soon.