Updated Jan 2023 - How to Use RStudio with ESSENCE API Guide

This RStudio API guide provides an overview of the ESSENCE APIs and how to access them through RStudio. We will begin with a very brief explanation of application programming interfaces (APIs), then list what APIs are available in ESSENCE, and finally expose you to basic examples of R code and packages so that you can start using RStudio to access ESSENCE data, create your own R Markdown reports and Shiny applications, or do exploratory analyses not possible within ESSENCE. 

February 16, 2021

UPDATED: Syndromic Surveillance 101 - Introduction to R for Health Surveillance

In this 26 minute video, Eric Bakota offers an overview of a free statistical package, R, and an overview of commonly used tips and tricks shared in the surveillance community for analysis work in R.

Objectives:

April 30, 2019

Using databases and dplyr to work with data in R

Presenter April 30, 2018.

April 30, 2018

Analyze US Census Data in R with tidycensus

Presented February 19, 2018.

February 19, 2018

Leveraging the NSSP R Studio Server to Automate QA Monitoring and Reporting

In 2016, the CDC funded 12 states, under the Enhanced State Opioid Overdose Surveillance (ESOOS) program, to utilize SyS to increase timeliness of state data on drug overdose events. In order to operationalize the objectives of the grant, there was a need to assess and monitor the quality of Kentucky’s SyS data, with limited resources. We leveraged the NSSP’s R Studio Server to automate quality assurance (QA) monitoring and reporting to meet these objectives.

Objective:

January 25, 2018

R Group for Biosurveillance

Mission

The mission of the R Group for Biosurveillance is to connect R users and Advance the Practice of R in Public Health Surveillance

Objectives

December 28, 2018

SaTScan Tutorial

SaTScan software is used widely in outbreak detection.  It's free, flexible, and fast.  However, it is somewhat cumbersome, in that access is primarily through a GUI.  While this is probably best for occasional use, it does not lend itself to automated analysis, storage and re-use of surveillance results, or to methodological investigations of the properties of the methods implemented in SaTScan.  
 

May 20, 2019

A Tool for Interactive Disease Outbreak Visualization, Detection, and Forecasting

Interactive tools for visualization of disease outbreaks has been improving markedly in the past few years. With the flagships Google Flutrends1 and HealthMap2 providing prime examples. These tools provide interactive access to the general public concerning the current state-of-affairs for disease outbreaks generally and specifically for influenza. For example, while browsing HealthMap I learned of a case of tuberculosis on my campus, Iowa State University. While extremely sophisticated, these tools do not utilize modern statistical algorithms for detection or forecasting.

August 22, 2018

R Software Environment Resources

What is R?

R is a language and free software environment for statistical computing and graphics. It compiles and runs on a variety of UNIX platforms, Windows, and MacOS. It is similar to the S language and environment - in fact, much code written in S will run unaltered in R. The R environment is an integrated suite of software facilities for data manipulation, calculation and graphical display. You can learn more about R from the R Project website. 

How Can I Get R?

October 27, 2017

An exploratory analysis of the 2010 measles outbreak in Zimbabwe

This report describes an exploratory analysis of the 2009-2010 Zimbabwe measles outbreak based on data publicly available in the World Health Organization's Zimbabwe cholera epidemiological bulletin archive. As of December 12th 2010, the outbreak appears to have ended after it is suspected to have caused 13,783 infections, 693 of those being confirmed IgM positive, and 631 deaths.

Objective

May 02, 2019

Pages

Contact Us

NSSP Community of Practice

Email: syndromic@cste.org

 

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