hubEnsemblesManuscript

This repository contains the data and code for our paper:

Li Shandross, Emily Howerton, Lucie Contamin, Harry Hochheiser, Anna Krystalli, Consortium of Infectious Disease Modeling Hubs, Nicholas G. Reich, Evan L. Ray (in prep). Multi-model ensembles in infectious disease and public health: Methods, interpretation, and implementation in R. https://doi.org/10.1101/2024.06.24.24309416v2

How to cite

Please cite this compendium as:

Li Shandross, Emily Howerton, Lucie Contamin, Harry Hochheiser, Anna Krystalli, Consortium of Infectious Disease Modeling Hubs, Nicholas G. Reich, Evan L. Ray (in prep). Compendium of R code and data for Multi-model ensembles in infectious disease and public health: Methods, interpretation, and implementation in R. Accessed 06 Oct 2025. Online at https://doi.org/10.5281/zenodo.17259775

Contents

The analysis directory contains:

• 📁 paper: Quarto source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis. It also has a rendered version, hubEnsembles_manuscript.html, suitable for reading (the code is replaced by figures and tables in this file)
• 📁 data: Data used in the analysis.
• 📁 figures: Plots and other illustrations

How to run in your browser or download and run locally

This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software itself and optionally RStudio Desktop.

You can download the compendium as a zip from from this URL: master.zip. After unzipping:

• Open the .Rproj file in RStudio
• Run devtools::install(dependencies = TRUE) to ensure you have the packages this analysis depends on (also listed in the DESCRIPTION file). You might need to install devtools first by running install.packages("devtools").
  • A renv.lock with the exact versions of packages used is also present in the repository
• Finally, open analysis/paper/hubEnsembles_manuscript.qmd and knit to produce the hubEnsembles_manuscript.html, or run rmarkdown::render("analysis/paper/hubEnsembles_manuscript.qmd") in the R console

Licenses

Text and figures : CC-BY-4.0

Code : See the DESCRIPTION file

Data : CC-0 attribution requested in reuse