A collection of PySCeS Markup Language files and Python helper functions.
##Contents:
###PML Model Descriptions Ecology:
- LV.psc : Basic Lotka-Volterra model
- LV_queue.psc : Basic Lotka-Volterra model with queue-based predator creation
- SILV.psc : Susceptible-Infected process with predation
- TwoPreyLV.psc : Basic Lotka-Volterra model with two prey species
- logisticLV.psc : Basic Lotka-Volterra model with logistic-growth of prey species
- logisticLV_queue : Basic Lotka-Volterra model with logistic-growth of prey species and queue based predator creation.
Epidemiology:
- SIR.psc : A basic SIR epidemic model with no demographics
- SIR_BirthDeath.psc: A basic SIR epidemic model with demographics
- cdiff_FT.psc : A model of fecal microbiota transplantation to prevent healthcare facility-associated C. difficile infection and recurrence.[1]
- cdiff_FT_queue.psc : The fecal microbiota transplantation model with queue-based admissions and discharges.
###Known Bugs/Notes:
- Birth/death model currently produces an integration error for some values of mu ~ 25000. This error can be reproduced in SciPy using odeint. SciPy's ode.integrate and R both solve the system just fine - this appears to be a fleeting stiffness problem. Haven't tried this with other PySCeS solvers.
- LV.psc can result in very long run-times when simulated stochastically, due to exponential prey growth if the predator species experiences stochastic extinction.
###References [1] E.T. Lofgren et. al. A Mathematical Model to Evaluate the Routine Use of Fecal Microbiota Transplantation to Prevent Incident and Recurrent Clostridium difficile Infection. Infection Control and Hospital Epidemiology, Vol. 35, No. 1 (2014) pp. 18-27 http://www.jstor.org/stable/10.1086/674394