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