This repository contains the code required to reproduce the results from the study Chan et al. 2026.
For this demonstration, we analyze data from the 2010/2011 to 2023/2024 seasons. This analysis generates results for two main phases: the pre-COVID-19 period (2010/2011–2019/2020) and the post-COVID-19 period (2022/2023–2023/2024), as well as for 14 individual seasons.
In the R/figure folder, we have uploaded the main figures as presented in our manuscript. Users can also generate all figures by running the script R/0_main.R.
The script R/0_main.R contains functions for analyzing surveillance data using parallel processing. The analysis workflow includes data processing (imputation and smoothing), time series clustering, and spatial autocorrelation analysis of peak timing.
The surveillance data utilized in this study are publicly available through the CDC's FluView Interactive platform https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html. All analyses were performed using R version 4.4.0. The R scripts and code supporting the findings of this study are accessible on GitHub at https://github.com/CDCgov/influenza-cluster-us.
The conclusions, findings, and opinions expressed by authors contributing to this article do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions.
Louis Yat Hin Chan, PhD, MSc
CDC Steven M. Teutsch Prevention Effectiveness (PE) Fellow – Analytics and Modeling Track, Class of 2023
Applied Research and Modeling (ARM) Team
Epidemiology and Prevention Branch (EPB)
Influenza division (ID)
National Center for Immunization and Respiratory Diseases (NCIRD)
Centers for Disease Control and Prevention (CDC)
Work address: 1600 Clifton Road, Atlanta, GA 30329
Work email: LouisChan@cdc.gov
This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.
You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
The source code forked from other open source projects will inherit its license.
This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/other/privacy.html.
Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.
All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.
This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.
Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.