hhh4-workshop

Workshop on hhh4 and the endemic-epidemic framework

Prerequisites for tutorial part of hhh4 workshop:

To participate in the tutorial session you will need a computer with the statistical analysis software R installed. R can be downloaded and installed from https://cran.r-project.org/. You need to install the packages "surveillance" and "hhh4addon". In the tutorial it will be assumed that you have installed R and the required packages.

To install the packages run the commands:

install.packages("surveillance")
remotes::install_github("jbracher/hhh4addon")

Once the package is installed, you can load it via

library(surveillance)

If you attempt to load a package without first installing it you should encounter an error message along the lines of

Error in library(surveillance) : there is no package called ‘surveillance’

Please note that certain packages require specific versions of R. You may end up with an error message like

Warning in install.packages :
  package ‘<package name>’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

For a description of the surveillance package run the command

package?surveillance

To run the code for the tutorials, clone or download this repository onto your machine using the green button at the top of this page. Open R/RStudio and change the working directory to wherever you cloned/downloaded the repository. Read the tutorial instructions and open the R script provided for the tutorial to execute the code line by line.

Further reading

• https://surveillance.R-forge.R-project.org/ (package website)
• The package vignettes vignette("hhh4") and vignette("hhh4_spacetime")
• Two case studies on hhh4-based forecasting
• List of published applications of the endemic-epidemic modelling frameworks
• Tutorials for the surveillance package