ExcessILI

ExcessILI facilitates formatting line list data from syndromic surveillance datasets into time series, and enables analysis of these data to detect increases in reporting above the seasonal baseline. For US data, there is an option to automatically adjust the data for state-specific flu activity (using data from NREVSS and/or state-specific RSV activity (based on Google search volume). The user can either start with line list data, or formatted time series data. An rshiny app is provided to examine data products.

Installation

# Currently, ExcessILI is not availble on CRAN
# install.packages("ExcessILI")

# Install development version from GitHub. This requires that the 'devtools'
# package be installed.
if (!require("devtools")) {
  install.packages("devtools")
}
devtools::install_github("weinbergerlab/ExcessILI")

Usage

  • To see how to go from line list data to an interactive app, see vignette("ESSENCE")

  • For an example of how to use the analysis functions with CDC ILINet data, see vignette("ILINet").

  • For preliminary results on pneumonia and influenza mortality increases above the seasonal baseline, visit vignette("PImortality")

Resources