v2.2.1

Source code to accompany Smith et al. 2025, Royal Society Open Science: "Potential benefits of adaptive control strategies are outweighed by costs of infrequent, but dramatically larger disease outbreaks." Please find code for this manuscript under the USDOSv2.2.1_Flexible_Strategy branch.

Abstract

Understanding underlying transmission dynamics is necessary to effectively control an infectious disease outbreak. In the likely event that managers do not know where to target control resources because drivers of transmission are unknown, it may be desirable to to tailor control strategies to a given outbreak by implementing control actions gradually in response to changes in the outbreak (adaptive) rather than all at once (fixed). Adaptive control strategies may also prevent overreaction and thus causing unnecessary socioeconomic harm. However, it remains unclear whether the benefits of adaptive control strategies outweigh the potential of under-reacting and causing larger outbreaks. To weigh this trade-off, we used a validated national scale foot and mouth disease transmission model to compare how adaptive and fixed control strategies as well as various attributes of the control process affect outbreak size. We find that adaptive control strategies do not cost less for the vast majority of outbreaks, but infrequently result in much larger and more costly outbreaks due to decision-making time and case reporting lags. This study emphasizes the cost of under-reacting to a disease outbreak and that minimizing decision-making time should be a key consideration when developing outbreak response guidelines.

This release contains all necessary files to run USDOSv2.2.1 while some of these files may be absent from the USDOSv2.2.1 branch due to their size.

Repository Contents

• USDOSv2.2.1: United States Disease Outbreak Simulation (USDOS) version 2.2.1 module.
• Post_Processing: R scripts and files for processing USDOS simulation results.

Getting Started

To utilize the contents of this repository, follow these steps:

1. Run USDOSv2.2.1 Module:

   • Navigate to the USDOSv2.2.1 directory and follow the instructions in its README.md to run USDOS.

2. Place Output Files in Post_Processing/Files_To_Process:

   • After running USDOSv2.2.1, locate the generated output files in the USDOSv2.2.1 folder.
   • Place these files in the Post_Processing/Files_To_Process directory.

3. Run Post-Processing Module:

   • In the Post_Processing directory, execute the run_postProcessing_USDOSv2.2.1.R script.
   • This script will process the USDOS output files by generating datafiles, histograms, violin plots, and maps summarizing each simulation scenario.

For more detailed information on each component, refer to the README.md files within the respective subdirectories.

If you encounter any issues or have questions, please contact webblaboratory@gmail.com.