Set up template

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
+rsconnect/
+
+# Mac DS_Store files
+*.DS_Store

CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant
+(http://contributor-covenant.org), version 1.0.0, available at
+http://contributor-covenant.org/version/1/0/0/

LICENSE

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+MIT License
+
+Copyright (c) 2018 The Throughput Annotation Project
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![NSF-XXXXXXX](https://img.shields.io/badge/NSF-XXXXXXX-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=XXXXXXX) [![NSF-XXXXXXX](https://img.shields.io/badge/NSF-XXXXXXX-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=XXXXXXX)
+
+# Project Name
+
+A short, one paragraph description of the project goes here.
+
+  * Please add all project Award numbers to the Badges above.  This will allow us to crawl and add these repositories to the graph, and also show NSF that we are being good citizens.
+  * Please ensure that all contributors from Throughput have ORCIDs and that these are linked below in the contributors section.
+  * Please consider a clear directory structure early on, and report it below in the "How to use this repository".
+  * Please define which data products
+
+## Contributors
+
+This project is an open project, and contributions are welcome from any individual.  All contributors to this project are bound by a [code of conduct](CODE_OF_CONDUCT.md).  Please review and follow this code of conduct as part of your contribution.
+
+  * [Contributor Name1](http://example.com/contributor_url1) [![orcid](https://img.shields.io/badge/orcid-XXXX--XXXX--XXXX--XXXX-brightgreen.svg)](https://orcid.org/XXXX-XXXX-XXXX-XXXX)
+  * [Contributor Name2](http://example.com/contributor_url2) [![orcid](https://img.shields.io/badge/orcid-XXXX--XXXX--XXXX--XXXX-brightgreen.svg)](https://orcid.org/XXXX-XXXX-XXXX-XXXX)
+
+### Tips for Contributing
+
+Issues and bug reports are always welcome.  Code clean-up, and feature additions can be done either through pull requests to [project forks]() or branches.
+
+All products of the Throughput Annotation Project are licensed under an [MIT License](LICENSE) unless otherwise noted.
+
+## How to use this repository
+
+A description of the files and directory structure in the repository.
+
+### Workflow Overview
+
+Th project uses X core information, manages it and passes our some stuff.
+
+### System Requirements
+
+This project is developed using (Python? R?).  It runs on a Windows system (?).  Continuous integration uses TravisCI (?).
+
+### Data Requirements
+
+The project pulls data from (?).
+
+### Key Outputs
+
+This project generates (an API, some log files, what?)
+
+## Metrics
+
+This project is to be evaluated using the following metrics. . .

data/README.md

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+# Project Data
+
+Project data is drawn from the following primary sources:
+
+  * Please list data sources
+  * . . .

figures/README.md

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+# Project Figures
+
+This folder is primarily for any project figures.

src/README.md

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+# Project Scripts
+
+Any scripts that are not the primary coding scripts should be placed in this folder, or may be organized by thematic sub-folders.