PopART-IBM an individual-based model for simulating HIV epidemic in high-prevalence settings, as used in the HPTN 071 (PopART) trial. A full description of the model is described in Pickles et al., 2020. A data dictionary describing all the output output files from the model is here and a data dictionary describing the parameters in the model is described here.
For Mac and Unix-type systems, PopART-IBM requires a C compiler (such as gcc) and the GSL libraries installed:
cd POPART-IBM/src
make allGSL can be downloaded from here.
For Windows systems, please see this walkthrough.
cd POPART-IBM/src
./popart-simul.exe <inputdir> <nruns>where
inputdir: Directory where input parameter files ("param_processed*.csv") are locatednruns: number of simulation runs in parameter files (num. of lines in parameter files to read in)
A basic example illustrates how the parameter input files can be set up (steps 1 and 2) as is expected by the model.
Notes
- Additional command-line arguments are described in main.c.
- The model will write all output files to the directory
inputdir/Output(additional command-line arguments can adjust this). - The output files written will depending upon which macros are set to 1 within the file constants.h (those beginning
WRITE_*).
Tests are written pytest using Python v3.6+, and run in the following manner: python3 -m pytest. Some tests take a long time to run and so are not run by default, they can be invoked using the --runslow option in pytest (python3 -m pytest --runslow).
It is recommended that tests are run under a Python virtual environment. The following will set up a Python virtual environment, install required modules, and run the tests:
python3 -m venv venv
source venv/bin/activate
python3 -m pip install -r tests/requirements.txt
python3 -m pytest
deactivate
Contributions are most welcome. Please see the documentation on contributing for further information. Please contact the core team or raise an issue before making a pull request.