Estimating the Direct Impact of Influenza Vaccination and Vaccine-Averted Illnesses Using an Extended Static Compartmental Model

Overview

This repository contains a Microsoft Excel tool with supporting R scripts to estimate the direct impact of influenza vaccination. The tool is an extension of the static compartmental model originally developed by Kostova et al., and builds on previous work documented in the background chapter of the WHO Burden of Disease manual and earlier versions of the tool.

A manuscript describing this extended tool is currently under development. This page will be updated with the citation once it is available.

Running the tool

1. Download the repository by clicking the green Code button and selecting Download ZIP. Extract the folder to a location on your machine.
2. Open Phase 2 data input tool_final.xlsm.
3. On the Inputs tab, follow the instructions to enter the required model parameters.
   • After completing all required inputs, click the Run model button.
   • The results will populate on the Results tab.
   • To generate confidence intervals for the results, the model must be run in R. Before proceeding, save the Excel file (do not change the file name) and close it.
4. Open the R project file Averted_Illness_PhaseII.Rproj to launch RStudio.
5. In RStudio, open Avert_Illness_Calculation.R and run the entire script. Results will automatically export to Phase 2 data input tool_final.xlsm.
6. (Optional) On the Scenarios tab, follow the instructions to input data for modeling different vaccine coverage and deployment scenarios.
   • After completing all required inputs, click the Run scenarios button.
   • The results will populate on the Scenario Results tab.

Tip: Use the Clear inputs button at any time to reset inputs.

Disclaimer

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.

Contact information

Young Moo (Daniel) Yoo, MSPH
Situational Awareness and Modeling (SAM) Team
Global Influenza Branch (GIB)
Influenza Division (ID)
National Center for Immunization and Respiratory Diseases (NCIRD)
Centers for Disease Control and Prevention (CDC)

Work address: 602 Webb Gin House Rd, Lawrenceville, GA 30045
Work email: opp8@cdc.gov

Public Domain Standard Notice

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.

License Standard Notice

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.

Privacy Standard Notice

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.

Contributing Standard Notice

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.

Records Management Standard Notice

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.

Additional Standard Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.