Code for simulating the metapopulation SEIR model. Sample network for US national simulation included.
A preliminary description of this model appeared in IEEE ICHI 2017: https://ieeexplore.ieee.org/document/8031141/
Journal version: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007111
Cite as: Venkatramanan S, Chen J, Fadikar A, Gupta S, Higdon D, Lewis B, Marathe M, Mortveit H, Vullikanti A. Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints. PLoS computational biology. 2019 Sep 16;15(9):e1007111.
The description of the model and a software manual can be found inside the doc/ folder.
PatchSim is compatible with both Python 2 and 3. It requires numpy and pandas.
Please use the different test*.py scripts to test the different functionalities of PatchSim. For more details on these features please check the software manual.
To test the US national simulation, extract the zip file test/US_county.zip and run "python test_det_US.py" from inside test/ folder.
This fork is under development to integrate features from EpiGrind to describe MPP exposures by mean person-hours of exposure daily, allowing for density-dependent transmission rates.