RSV_Flu_interaction_2022

This repository contains the data and code used to analyze RSV and Flu interaction in the United States.

Data

• FluView Data: accesed July 8, 2021 source: https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html
• RSV data request from NREVSS team
• Sequence data was obtained from GISAID.
• See also here.

Prerequisites

• R, and the R packages listed here.

Instructions

• In each folder:
  • In the root directory, start with sepecific order.
  • This figure.R contains all figures used in manuscript.

Additional Details

• BEAST was used for the analysis displayed in Figure 2. For details, see here.
• Time series analysis was conducted in here.
• Parameter estimation for statistical model was conducted in R on a cluster due to computational time considerations. For conveneience, this step can be by-passed and all the plots can be built from pre-computed R objects (located in model/results). See here for additional details.