Overview

This is the repository for the analysis of ""Estimating standard-dose and high-dose Fluzone vaccine efficacies for influenza A based on HAI titers". All analysis reproduction should be possible from this repo.

Repository Description

• All initial, "raw" data can be found in the data/raw-data folder
• All code used to conduct this analysis and generate results can be found in the code folder
• All generated results can be found in the results folder. The figures and tables folders contain all figures and tables presented in the main text and supplement, while the output folder contains .rds files with data sets generated through the analysis
• The files used to generate the main text and supplement of the manuscript can be found in the products/manuscript and products/manuscript/supplement folders, respectively
• More information as needed is provided in the README files within each folder

Analysis Replication

This project uses renv to help ensure reproducibility. Upon downloading the repository, running renv::restore() will download all used packages and dependencies in the versions used in conducting this analysis.

To completely replicate our analysis, run the code scripts in the following order:

1. processing-code.R
2. statistical-analysis.R
3. fig-gen.R
4. table-gen.R

The functions.R and objects.R scripts will each be called at the beginning of every script listed above, so they do not need to run explicitly. However, the functions.R script in particular contains the code responsible for much of the analysis, such as the VE and DVE calculations and bootstrapped CIs, so alterations to that part of the analysis would take place in that script.

The CDC reported estimates were initially directly webscraped from the CDC website. However, several of the seasons' pages have since been archived, altering the URLs used to access them. We have therefore placed the data set with CDC reported VE in the raw-data folder. All values can still be checked by accessing each season's reported VE and accompanying information at https://www.cdc.gov/flu/vaccines-work/past-seasons-estimates.html.