Epidemiology of Measles Cases, Operation Allies Welcome

The enclosed repository contains (1) reduced datasets and (2) analyses scripts to support findings reported in Masters et. al (2022).

Citation and Correspondence

Manuscript citation here.

Getting Started

TODOS 1. Use of repo 1. Installation of snakemake and general use of script for sequence assembly. 1. conda environments to support running the analyses 1. R markdowns as rendered notebooks 1. epi models, etc. 1. Links to NCBI 1. Links to SRA

Location

By default, you should use this to start a new project on CDC internal git server https://git.cdc.gov. Everyone in CDC has access to this when they are on network.

If you already have access, or anticipate people outside CDC needing to view or work on this code, use this to start a new project on CDC's private GitHub cloud, https://github.com/cdcent. You can request access. This is in the cloud so you can get to it off network.

If you have special requirements, you can check out the other locations (intranet only) where you can use this template.

Structure

These folders are meant to help organize and make it easier for others to understand and contribute.

sh ├── R <- R scripts, delete if unnecessary ├── SAS <- SAS scripts, delete if unnecessary ├── analysis <- analysis and visualization files (eg notebooks, tableau, Rmarkdown, etc ) │   └── template.Rmd <- example template for Rmarkdown ├── data <- data files used by project │   ├── clean <- processed files ready for analysis, try not to store these in the repo, make them │   ├── meta <- metadata needed for analysis │   └── raw <- raw files, original, immutable data dump ├── docs <- documentation and references (codebooks, etc) ├── output <- output files ├── python <- Python scripts, delete if unnecessary ├── readme.md <- Description of project, instructions for how to run ├── reports <- Generated reports and visualizations │   └── figures <- Generated graphics used in reports └── sql <- SQL scripts, delete if unnecessary

References

• https://github.com/lazappi/cookiecutter-r-analysis
• https://git.cdc.gov/oet5/premier_ehr
• https://git.biotech.cdc.gov/fya1/spock
• https://github.com/drivendata/cookiecutter-data-science

Housekeeping

This section contains info useful for organization.

• Point of contact: SRRG
• Organizational unit: EOC/SRRG
• Related projects: N/A
• Related investments: COVID-19 Response
• Governance status: Under design
• Program official: Brian Lee

The participants of this project are required to adhere to our code of conduct. Although the contents of this project are available under the Apache Software License distribution is restricted to only appropriate CDC staff due to cybersecurity regulations. Unless otherwise noted, all contributions to this project are accepted by the contributor as containing unlimited data usage rights by CDC and under the same license of the project.

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.

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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.

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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.