WHD model

To Build

g++ is the default compiler.

make

For more details please refer to the Makefile Or compile diretly by typing: ./make.sh

To Run

./build/bin/malaria_model -c config.json -o outputs

Mandatory Commandline Options

• -c [FILE], user specified simulation configuration file. A simplified (not complete) example config_whd.json is given below.

{
    "simulation" : {
        "schema_file_name" : "schema.config.json",
        "total_steps" : 60,
        "total_population" : 100
    },

    "whd" : {
        "whd_level" : 0,
        "II50" : 2000000000,
        "pmf" : 11.0,
        "gamma": 0.75,
                     
        "transition_matrix" : {
            "Jpk" : {
                "CL": 3.2500,
                "V2": 5.3750
            }
        }
    }
}

• -o [OUTPUT_DIRECTORY]

Optional Commandline Options

• -i [OUTPUT_PREFIX], if given will be used as prefix for all outputs of this run, otherwise a timestamp will be used to identify outputs.

To Test

We use the Catch2 framework.

1. Build tests:

make test
Or compile diretly by typing:
./make_4_test.sh

2. Run all tests:

malaria_model$ ./build/bin/test

3. List all tests:

malaria_model$ ./build/bin/test -l

4. Run a specific test:

malaria_model$ ./build/bin/test [whd:test]

malaria_model$ ./build/bin/test [whd_multiple:test]

Dependencies

C++ Libraries and the version installed on the development machine:

.hpp Dependencies

These are header-only libraries that are included as part of this project. No installation is required.

• Eigen, v3.3.9, for linear algebra / matrix operations. Included in include/third_party directory.
• Catch2, v2.1.2, a C++ test framework. ./test/third_party/

License

The WHD model is licensed under the GNU GENERAL PUBLIC LICENSE. See LICENSE for more information.

Author

Babak Mahdavi Ardestani

babak.m.ardestani@gmail.com