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:

1. Univariate forecasting of Swiss ILI counts using

   • forecast::auto.arima() --> vignette("CHILI_arima")

   • glarma::glarma() --> vignette("CHILI_glarma")

   • surveillance::hhh4() --> vignette("CHILI_hhh4")

   • prophet::prophet() --> vignette("CHILI_prophet")

   • experimental kcde::kcde() --> vignette("CHILI_kcde")

   • and MASS::fitdistr() for naive reference forecasts --> vignette("CHILI_naive")

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

Installation

To install the released HIDDA.forecasting package (with pre-built vignettes) together with other packages required to run the analyses:

# install.packages("remotes")
remotes::install_url("https://github.com/HIDDA/forecasting/releases/download/v1.1.2/HIDDA.forecasting_1.1.2.tar.gz", dependencies = TRUE)

Alternatively, to install HIDDA.forecasting from the current sources, building the vignettes on your machine, you could use:

# install.packages("devtools")
devtools::install_github("HIDDA/forecasting", dependencies = TRUE, build_vignettes = TRUE)

To browse the installed vignettes:

browseVignettes("HIDDA.forecasting")

Note that the "CHILI" vignettes include source("setup.R"), which refers to a small R script available from the installed package at

system.file("doc", "setup.R", package = "HIDDA.forecasting")