Rnssp

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")

To install the package for Webassembly, run the following in your webr REPL or add it to your shinylive application:

# Install the Rnssp package for webr
webr::install("Rnssp", repos = c("https://cdcgov.github.io/Rnssp-wasm", "https://repo.r-wasm.org"))

Usage

This is a basic example which shows you how to:

• use the Rnssp package to create a user profile
• and use the user profile to pull data from an API (here the ESSENCE API)

library(Rnssp)

## Creating a user profile (token)
myProfile <- create_token_profile()

## Creating a user profile (username and password)
myProfile <- create_profile()

## 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

@software{Azondekon_Rnssp_A_Signature_2024,
  author = {Azondekon, Gbedegnon Roseric and Sheppard, Michael},
  doi = {10.5281/zenodo.10884244},
  license = {Apache License (>= 2)},
  month = mar,
  title = {{Rnssp: A Signature R package for the National Syndromic Surveillance Program (NSSP)}},
  url = {https://github.com/CDCgov/Rnssp},
  version = {0.3.0},
  year = {2024}
}

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