Count Multiple Outbreak Detection System

Author: John Aronis, University of Pittsburgh

This project uses the Maven project management tool. Please install Maven before continuing to read this document. Maven can be downloaded from https://maven.apache.org/download.cgi.

To run CMODS, first build the executable jar file by executing the command: To create a runnable JAR file, execute the command:

mvn package

Once the package is built, run with:

java -jar target/cmods-1.0-SNAPSHOT-jar-with-dependencies.jar <file> <column> <startYear> <startWeek> 
                       <numberOfWeeks> <predictionYear> <predictionWeek> <population> <theta> <models>

For instance:

java -jar target/cmods-1.0-SNAPSHOT-jar-with-dependencies.jar src/test/resources/ILINet.csv ILITOTAL 2009 25 52 2009 32 300000000 0.10 100000

runs the system on the data file ILINet.csv, using column ILITOTAL, with 52 weeks of data starting at MMWR 25 in 2009, and a prediction on MMWR 32 of 2009, assuming population 300000000, 10% of ILI patients go to a physician, and search over 1000000 models.

The subdirectory src/test/resources contains a single csv file from the CDC (https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html) with ILINet data.

Funding Acknowledgement

Count-MODS is funded by the National Institutes of Health (NIGMS) program for Models of Infectious Disease Agent Study (MIDAS) grant U24GM110707.