Stride project

CodeFactor	Travis	Clang 5	GCC 6	GCC 7

Stride is an Open Source project to simulate transmission of infectious diseases.

The Stride acronym stands for Simulate transmission of infectious diseases.

The project is hosted in a GitHub code repository and has a continous integration
cycle build & test at Travis CI. The online reference documentation is automatically
generated with each new commit of the code.

The current status of the project build is :

The current release is Stride V1, 18.06.

Information on layout, installation, dependencies of the project, and platforms that
are supported, can be found in the files INSTALL.txt, DEPENDENCIES.txt and
PLATFORMS.txt respectively. For license info, see LICENSE.txt.

Current contributors are (in alphabetical order):

• Niels Aerens (@PurgingPanda)
• Thomas Avé (@thomasave)
• Tobia De Koninck (@LEDfan)
• Robin Jadoul (@RobinJadoul)

Contact Person:

• Name: Tobia De Koninck
• Github: (@LEDfan)
• E-Mail: tobia.dekoninck@student.uantwerpen.be

Upstream:

• Jan Broeckhove (jan.broeckhove@uantwerpen.be)
• Elise Kuylen (elise.kuylen@uantwerpen.be)
• Lander Willem (lander.willem@uantwerpen.be)

GenGeo

The GenGeo can be tested by compiling Stride and then running the ./cmake-build-release/installed/bin/gengeopop program. This executable can be given some files as parameter (use gengeopop --help to show the usage), these paths are relative to the data directory. By default the program will use the following files:

• flanders_cities.csv
• flanders_commuting.csv
• households_flanders.csv The GeoGrid will be written into gengeopop.json, which can be opened using the MapViewer.

GenGeo MapViewer

The MapViewer is compiled with the other binaries. It can run by ./cmake-build-release/installed/bin/mapviewer. You then have to load a geogrid file by clicking the load file button on the right hand side. The map on the left hand side shows all the locations in the geogrid. You can get more info by clicking on a marker. The middle column will then have the info about the location and the contact centers. You can click on one of the contact centers in that list, you will then get info about it in the right column. You can select multiple locations by using SHIFT.

Calibration tool

The calibration tool can be run by ./cmake-build-release/installed/bin/calibration. This will first compute the exact values for the scenario tests, then compute the mean and standard deviation for each testcase by running it multiple times using different seeds, and finally show a boxplot of the results using QtCharts.

Integration

The Stride binary can use a Population in three ways:

• default Generate a Population using PopulationBuilder (use ./bin/stride)
• import Import a Population from a proto or json file, which was generated using gengeopop. (use ./bin/stride -c run_import_default.xml)
• generate Generate a Population using GenGeoPop and provide data files and parameters. (use ./bin/stride -c run_generate_default.xml)