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R Studio

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. 

Submitted by hmccall on

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.  

 

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

To systematically organize the World Health Organization data on the 2010 measles outbreak in Zimbabwe. To perform a post-hoc exploratory analysis to understand how the outbreak spread geographically and evaluate the effectiveness of a mass vaccination campaign.

Referenced File
Submitted by elamb on
  • Why the syndrome was created? This syndrome was created to monitor tick related emergency room visits using regular expressions in R. 
  • Syndromic surveillance system (e.g., ESSENCE, R STUDIO, RODS, etc.) Data collected from Epicenter, but parsed and analysed in R/Rstudio
  • Data sources the syndrome was used on (e.g., Emergency room, EMS, Air Quality, etc.) Emergency room and Urgent Care
Submitted by Anonymous on

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. In addition, the development cost and perhaps the maintenance cost is not trivial. We aim to build a similar visualization tool that incorporates modern algorithms for detection and forecasting but has low development and maintenance cost. Due to the low cost this tool is appropriate for quick deployment in developing countries for emerging outbreaks as well as public health agencies with declining operating budgets.

Objective

To build a zero-cost tool for disease outbreak visualization, detection, and forecasting incorporating modern tools.

Submitted by knowledge_repo… on

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:

The aim of this project was to develop a nimble system to both monitor and report on the quality of Kentucky emergency department syndromic surveillance (SyS) data at system-wide and facility levels.

Submitted by elamb on

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?

Submitted by elamb on
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