This document has completed governance review per local and agency processes. This material is a draft.
This project is a repository housing R functions and scripts used in the US Centers for Disease Control and Prevention (CDC) COVID-19 Response International Task Force (ITF) COVID-19 Dashboard
As part of the CDC COVID-19 Response, the ITF Situational Awareness & Visualization (SAVI) Team has created and maintains an interal Power BI Dashboard to assist Task Force and response leadership with situational awareness of the global pandemic and response. The dashboard contains analyses of the most updated global case and testing data from multiple sources. The Power BI report that generates the dashboard runs multiple R scripts in order to refresh, process and update the data as CSV files which are then imported into Power BI for visualizations. The R functions in this project are used to read in case and testing data, apply algorithms and populate the underlying data tables of the report. Access to this dashboard is currently limited to CDC staff only.
The ITF has also created several curated Power BI views of global data on the public CDC COVID Data Tracker (https://covid.cdc.gov/covid-data-tracker/#global-counts-rates) to communicate to the general public the types of analyses that CDC is conducting using international data. The code saved to this repository would be used to populate the data underlying those views in a Power BI Dashboard.
Each function that produces a final analytic data set for visualization has been run in the "demo.R" script. These data sets can then be analyzed and visualized directly in R, or imported into Power BI to replicate the visuals produced by the ITF. More information can be found in the description.md file in the Rfunctions folder.
In addition, the "hotspot" trajectory code functions that classify epidemic curve status based on the incidence and rate of change have been separated so that they can be run using any data set that has been formatted properly. For instructions on how to run this code, see the [how to use hotspot code using your own data.md"]("./Rfunctions/how to use hotspot code using your own data.md") document in the Rfunctions folder.
The project uses several publicly-available data sources, including:
the COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University, cases and Deaths data sets:
More info here: https://github.com/CSSEGISandData/COVID-19
and here: https://coronavirus.jhu.edu/map.html
Citation: Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Inf Dis. 20(5):533-534. doi: 10.1016/S1473-3099(20)30120-1
https://covid19.who.int/WHO-COVID-19-global-data.csv More info here: https://covid19.who.int/
https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv
More info here: https://ourworldindata.org/coronavirus-testing
Even more info here: https://github.com/owid/covid-19-data/blob/master/public/data/README.md
Citation: Max Roser, Hannah Ritchie, Esteban Ortiz-Ospina and Joe Hasell (2020) - "Coronavirus Pandemic (COVID-19)". Published online at OurWorldInData.org. Retrieved from: 'https://ourworldindata.org/coronavirus' [Online Resource]
More info here: https://www.finddx.org/covid-19/test-tracker/
https://www.cia.gov/library/publications/the-world-factbook/fields/335rank.html
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 inthe 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 Surveillance Platform Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/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 are subject to the Presidential 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.