/Rnssp

A Signature R package for the National Syndromic and Surveillance Program (NSSP) at the Centers for Disease Control and Prevention (CDC). A collection of tools, functions, and Rmarkdown templates that supports the Community of Practice of the NSSP.

Primary LanguageRApache License 2.0Apache-2.0

Rnssp

Rnssp Pipeline Project Status: Active - The project has reached a stable, usable state and is being actively developed. Lifecycle: stable DOI

Overview

The Rnssp R package is a catalog of data processing and analytics tools, templates, and functions commonly used across the National Syndromic Surveillance Program at the Centers for Disease Control and Prevention (CDC). Its goal is to improve code reproducibility, standardize and document reusable functions, facilitate the sharing of routine reports across the NSSP Community of Practice (CoP), and better engage the NSSP CoP.

Installation

You can install the development version of Rnssp from GitHub:

# install the Rnssp package
devtools::install_github("cdcgov/Rnssp")

Usage

This is a basic example which shows you how to:

  • use the Rnssp package to create an NSSP user profile
  • and use the NSSP user profile to pull data from ESSENCE via the ESSENCE API
library(Rnssp)

## Creating an NSSP user profile
myProfile <- Credentials$new(
  username = askme("Enter your username: "), 
  password = askme()
)

## Inspect your `myProfile` confirming that username and password are completely hidden
myProfile

## JSON URL from ESSENCE API
url <- "https://essence.syndromicsurveillance.org/nssp_essence/api/alerts/regionSyndromeAlerts?end_date=31Jan2021&start_date=29Jan2021"

## Update Start and End dates in ESSENCE API URL
url <- change_dates(url, start_date = Sys.Date() - 30, end_date = Sys.Date())

## Pull Time Series Data from ESSENCE
api_data <- get_api_data(url) # or api_data <- myProfile$get_api_data(url)

## Inspect data object structure
names(api_data)

## Get a glimpse of the pulled dataset
glimpse(api_data$regionSyndromeAlerts)

Contributing to this project

Should you want to contribute to this project, submit a push request to this Github repository and consider submitting a request to be added as a developer to gazondekon@cdc.gov.

Getting Help

If you encounter a clear bug, please consider emailing the author at gazondekon@cdc.gov and/or file an issue with a minimal reproducible example.

Citing the Rnssp package

citation("Rnssp")

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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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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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.