POPART-IBM
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PopART-IBM is an individual-based model for simulating HIV epidemics in high-prevalence settings, as used in the HPTN 071 (PopART) trial. Using the default parameters, the model simulates approximately 50,000 individuals over several decades following demographic patterns from UN's Population Division.
For Mac and Unix-type systems, PopART-IBM requires a C compiler (such as gcc) and the GSL libraries installed:
GSL can be downloaded from here.
For Windows systems, please see this walkthrough.
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
inputdir/Output
(additional command-line arguments can adjust this). WRITE_*
). Tests are written pytest
using Python version 3.6 or later, and run in the following manner:
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
:
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:
The model has been published in several journals and conferences:
Contributions are most welcome. Please see the documentation on contributing for further information. The C code is documented using formatting for Doxygen. Please contact the core team or raise an issue before making a pull request.