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.