influenzaB_PNAS_2021

This repository contains the data and code used to analyze the 2019/2020 influenza season in the United States.

Data

• FluView Data: most recently accesed Febrary 28, 2020.
• FluView Data: accesed January 31, 2020, February 4, 2020 source: https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html
• Sequence data was obtained from GISAID.
• See also here.

Prerequisites

• R, and the R packages listed here.
• Note: the tinytex package requires a local install (once per machine). See https://yihui.org/tinytex/

Instructions

• In R:
  • In the root directory, run source("0build.R").
  • This file calls "0make.R" to run R analyses and generate R figures.

Additional Details

• For details regarding extra files see here.
• BEAST was used for the analysis displayed in Figure 3. For details, see here.
• Time series analysis (including phase and autoencoder) was conducted with python. Jupiter notebooks are provided in extra/time-series-analysis. The results are located in extra/data-phase and extra/figure-si.
• Parameter estimation 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 extra/data-pomp). See here for additional details.