Modelling scenarios of importation of H5N1 in the UK and the impact of interventions

This repository contains the code to reproduce the analyses of: Ward et al. (2024) Estimates of epidemiological parameters for H5N1 influenza in humans: a rapid review. https://doi.org/10.1101/2024.12.11.24318702..

Package structure

The package is organised into analysis scripts in the scripts/ folder, the plots included in the paper are in the plots/ folder.

library(fs)
fs::dir_tree()
#> .
#> ├── LICENSE
#> ├── R
#> │   └── utils.R
#> ├── README.Rmd
#> ├── README.md
#> ├── data
#> │   ├── H5N1pptdat.xlsx
#> │   ├── si_param_summary.csv
#> │   ├── si_posteriors.csv
#> │   └── si_raw_data
#> │       ├── index.csv
#> │       └── serial.csv
#> ├── h5n1_uk_scenario_modelling.Rproj
#> ├── plots
#> │   ├── CFR_review.png
#> │   ├── H7N7_R.png
#> │   ├── R0_US.png
#> │   ├── R0_review.png
#> │   ├── empirical_outbreak_size.png
#> │   ├── inc_review.png
#> │   ├── lat_inf_review.png
#> │   ├── outbreak_length.png
#> │   ├── outbreak_size.png
#> │   ├── serial_review.png
#> │   └── sero_review.png
#> ├── posterior_predictive
#> │   └── dt_draws.rds
#> └── scripts
#>     ├── fit_R_H5N1_US.R
#>     ├── fit_R_H7N7.R
#>     ├── fit_si_distributions.R
#>     ├── outbreak_distribution.R
#>     └── rapid_review_forest_plots.R

Analyses

H5N1 Epidemiological Parameter Rapid Review

The data for the epidemiological parameters collected from the rapid review are stored in the data/ folder in the H5N1pptdat.xlsx file.

These parameters are used to produce the forest plots that can be found in the plots/ folder. These plots have the name *_review.png, e.g. inc_review.png for the incubation periods.

The R script to produce all of the forest plots is the rapid_review_forest_plots.R file in the scripts/ folder.

Reproduction Number Estimation

The scripts to estimate the posterior distribution H5N1 data and H7N7 data are in fit_R_H5N1_US.R and fit_R_H7N7.R, respectively. Both in the scripts/ folder.

The posterior distribution plots for the reproduction number estimates are both in plots/: R0_US.png and H7N7_R.png.

Outbreak size distribution

The script to run the outbreak size and length distribution simulation and generate the plots is in scripts/outbreak_distribution.R. The plots are included in the plot folder, including the The outbreak_size plot and outbreak_length plot.

Other branches

This repository contains other branches which contain code that was written in the process of developing and writing this manuscript. Here we briefly describe these branches:

• bp_report: This branch contains a report that was written to develop the outbreak distribution analysis and plots while the number of cases reported in the US was increasing during the second half of 2024. It was used as a basis for the outbreak distribution analysis included in the paper but is not itself included as part of the publication. It is not actively updated and the paper should be referred to for the most up-to-date information.

• deprecated-models: This branch includes scripts and functions to run a travel testing model. This was developed while the project was being formulated, but was not included in the final version of the manuscript. The code remains on this branch, to potentially be used for a future analysis.

Known issues

When running:

pcd_model <- pcd_cmdstan_model()
# Error: CmdStan path has not been set yet. See ?set_cmdstan_path.

The fix is:

# Fix
cmdstanr::install_cmdstan()