Tools, Functions, Shapefiles data, and Rmarkdown templates to work with Syndromic Surveillance data

The National Syndromic Surveillance Program (NSSP) at the Centers for Disease and Control has a large Community of Practice (CoP) including states and local Departments of Health. The NSSP has developed multiple resources including analysis reports, analytic tools, and assisted with scripts to interface with ESSENCE. The Rnssp R package is built in an attempt to improve reusability, reproducibility, and distribution of the analytical resources developed at the CDC NSSP.

Rnssp functions

The Rnssp functions include:

API functions to pull data from the ESSENCE system or any REST API service
Various utility functions to securely set user credentials, add or remove R Markdown templates, or set new dates in API urls.
Anomaly detection and Time Series Trend classification algorithms
A feature to extend the package installation with NSSP custom-built parameterized R Markdown templates
Utilities to run custom-built shiny apps provided by NSSP

Rnssp vignettes

The vignettes serve as instructive tutorials demonstrating practical uses of the Rnssp package. Please run the Rnssp_vignettes() function to browse all available vignettes.

Rnssp Rmarkdown templates

By default, the Rnssp package comes with one R Markdown template. We leave it up to users to decide which template to extend the package with post-installation. To list all available template, run the list_templates() function. Please, check the Rnssp R markdown template Github repository at https://github.com/cdcgov/rnssp-rmd-templates.

Rnssp Shiny Applications

The Rnssp package comes with one custom-built Rnssp Shiny application. Users may run Rnssp custom-built shiny applications via Rnssp Rstudio addins or via the run_app() utility function. To list all available Rnssp shiny apps, run the list_apps() function. Please, check the Rnssp-shiny-appse Github repository at https://github.com/cdcgov/rnssp-shiny-apps.

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