The R package ‘HIDDA.forecasting’

The Handbook of Infectious Disease Data Analysis (Chapman & Hall/CRC, 2019) contains a chapter on “Forecasting Based on Surveillance Data” (preprint) by Leonhard Held and Sebastian Meyer. The R package HIDDA.forecasting provides the data and code to reproduce results from the two applications presented in that chapter.

Vignettes

1. Univariate forecasting of Swiss ILI counts from vignette("CHILI")

   Method	Article
   forecast::auto.arima()	vignette("CHILI_arima")
   glarma::glarma()	vignette("CHILI_glarma")
   surveillance::hhh4()	vignette("CHILI_hhh4")
   prophet::prophet()	vignette("CHILI_prophet")
   kcde::kcde()	RShowDoc("extra/CHILI_kcde", package="HIDDA.forecasting")
   MASS::fitdistr()	vignette("CHILI_naive")

2. Age-stratified analysis of norovirus counts in Berlin using surveillance::hhh4()
   → vignette("BNV")

Installation

• Download and install the R package tarball from the latest release, for example:

  ## install.packages("remotes")
  remotes::install_url("https://github.com/HIDDA/forecasting/releases/download/v1.1.3/HIDDA.forecasting_1.1.3.tar.gz")

• Or use the automated builds from https://ee-lib.r-universe.dev/HIDDA.forecasting:

  setRepositories(name = "CRAN", addURLs = "https://ee-lib.r-universe.dev")
  install.packages("HIDDA.forecasting")

To also install all other R packages required to reproduce the vignettes on your own system, add the argument dependencies=TRUE.

To browse the vignettes after installation:

browseVignettes("HIDDA.forecasting")

Note that the “CHILI” vignettes do source("setup.R"), using a small R script available from the installed package at system.file("doc", "setup.R", package="HIDDA.forecasting").