Welcome to VGsim’s documentation!
VGsim is the Python package for simulation of viral genealogies in the world-scale pandemic scenarios designed primarily for research purposes. Key VGsim features include
scalability and efficiency: optimized Guillespe algorithm over compartmental model generates epidemiological process; genealogy (transmission chain) is simulated only for sampled cases;
pathogen evolution and epistasis (through single nucleotide substitutions): each haplotype properties (e.g. transmission rate, recovery rate, triggered host immunity) can be set independently;
host immunity: different immunity types can have lower or higher susceptilibities to different haplotypes;
population model: demic model with migration (migration is modelled as short-term travels);
contact density (to reflect social, cultural and other population differences) and lockdowns.