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.
To describe an R package that was designed to provide ready implementation of veterinary syndromic surveillance systems, from classified data to the generation of alerts and an html interface.
Introduction
Introduction
The field of veterinary syndromic surveillance (VSS) is developing fast, with countries exploring a great variety of data sources. After implementing two VSS systems we have demonstrated that the steps from classified data to full system implementation can be streamlined, and published a guideline for implementation. All the steps described have been made available in an R package (https:// github.com/nandadorea/vetsyn). We aim to demonstrate the utility and potential of this streamlined approach.
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?