sempwn / cr0eso

Bayesian SEIR model fitting to multiple facility outbreaks

cr0eso

Covid r0 estimation of outbreaks (Cr0eso). R0 estimation of multiple outbreaks using an SEIR model

The package name comes from the Welsh word for "welcome"

Overview

cr0eso fits a Bayesian hierarchical SEIR (susceptible, exposed, infected, recovered) to a collection of outbreak data from different facilities.

Installation

Before installation, you will need a C++ compiler installed to compile the Stan model. If you are on a Mac or Linux, follow these instructions. If you are on Windows, follow the instructions here.

The following must return TRUE before continuing:

# install.packages("pkgbuild")
pkgbuild::has_build_tools(debug = TRUE)

Then, install the cr0eso package with:

# install.packages("remotes")
remotes::install_github("sempwn/cr0eso")

See the example in ?seir_model_fit and the vignette.

To install the package with the vignette:

remotes::install_github("sempwn/cr0eso", build_vignettes = TRUE)

and run:

browseVignettes("cr0eso")

Data

Data for facility outbreaks in BC is now included in the package, and can be found within the /data/ folder, or in the docs.

See the Changelog for any more updates to the package including new data.