Stride project

Stride is an Open Source project and its 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 :

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.

A breakdown of project artefacts (excluding third-party material) generated with the
cloc tool on 12/05/2018:

Language	files	blank	comment	code
C++	60	777	1463	3713
C/C++ Header	88	950	2450	2552
Python	26	266	388	847
R	6	322	353	729
CMake	20	103	602	572
YAML	2	17	22	126
Markdown	5	36	0	99
make	1	20	39	99
Bourne Again Shell	2	17	40	92
SWIG	5	19	12	65
XML	2	4	0	56
Bourne Shell	3	23	65	54
XSLT	1	8	0	36
--------	--------	--------	--------	--------
SUM:	221	2562	5434	9040

Current contributors are (in alphabetical order):

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

and contributing students

• Niels Aerens
• Thomas Avé
• Tobia De Koninck
• Robin Jadoul

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.

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)