https://github.com/babak2/whd
Within Host Dynamics
https://github.com/babak2/whd
cpp individual-based-modelling infectious-disease-modeling malaria-modeling pk-pd-modelling
Last synced: 2 months ago
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Within Host Dynamics
- Host: GitHub
- URL: https://github.com/babak2/whd
- Owner: babak2
- License: other
- Created: 2023-06-03T20:05:37.000Z (almost 2 years ago)
- Default Branch: master
- Last Pushed: 2023-11-21T19:03:50.000Z (over 1 year ago)
- Last Synced: 2025-02-01T19:45:12.297Z (4 months ago)
- Topics: cpp, individual-based-modelling, infectious-disease-modeling, malaria-modeling, pk-pd-modelling
- Language: C++
- Homepage:
- Size: 18.8 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# 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](https://github.com/catchorg/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](https://eigen.tuxfamily.org), v3.3.9, for linear algebra / matrix operations. Included in include/third_party directory.
- [Catch2](https://github.com/catchorg/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