This repository contains the data and code used to analyze the 2019/2020 influenza season in the United States.
- 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.
- R, and the R packages listed here.
- Note: the tinytex package requires a local install (once per machine). See https://yihui.org/tinytex/
- In R:
- In the root directory, run
source("0build.R"). - This file calls "0make.R" to run R analyses and generate R figures.
- In the root directory, run
- 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 inextra/data-phaseandextra/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.