Flusight-baseline

The code in this repository creates the Flusight-baseline model in the Flusight-forecast-data repository.

Dependencies

The baseline model is implemented in R, and has the following package dependencies:

• Packages available on CRAN:
  • purrr
  • dplyr
  • readr
  • tidyr
  • lubridate
  • ggplot2
  • ggforce
• Other packages, to be installed via GitHub:
  • covidHubUtils: See this package's documentation page for installation instructions.
  • simplets: Install from GitHub using the command devtools::install_github("reichlab/simplets")

Running the baseline model

The script baseline.R creates the baseline forecasts. It can be run, for example, via

Rscript baseline.R

The script fit_baseline_one_location.R contains some helper functions and does not need to be run directly.

Baseline forecasts will be saved in the directory weekly-submission/forecasts/Flusight-baseline, and forecast plots will be saved in weekly-submission/plots/Flusight-baseline.