This is an agent-based model that simulates the spread and potential persistence of a disease in an animal population (potentially including humans).
The original idea was derived from my work on chronic wasting disease when I was a postdoctoral researcher at the University of Illinois, and the current R code (/R/old/simDeer.R) is complete and based on that scenario. I am currently rewriting the code in Python, with the intention of making it more generalizable. I may eventually rewrite the R code to make it cleaner as well.
If I get really ambitious, I may one day animate the simulation....
In the case of the original deer model each iteration of the model represents a single year. In the course of the year, the following events happen, by calling the following methods:
- Initialize population:
Population()(Population.__init__()) - Plot initial distribution:
Population.plot()
Iterative sequence begins here:
- Disperse (young leave the mothers):
Population.disperse() - Plot new distribution
TODO:
- Calcualate home ranges:
Populaton.calculate_ranges()[possibly private] - Plot ranges
- Initialize soil matrix (distribution of infectious material in the environment:
Soil()(Soil.__init__()) - Soil Plot (Heat map of infectious material):
Soil.plot() - Infect (allow new animals to become infected as a function of distance to infected animals and probability of disease spread):
Population.infect() - Plot showing newly infected animals
- Infect soil (allow infected animals to leave contaminants in the soil):
Population.infect_soil() - Plot soil status
- Migrate back to winter grounds:
Population.migrate('winter') - Plot
- Infect soil
- Soil plot
- Animal-to-animal infection
- Soil-to-animal infection
- Plot animals
- Plot soil
- Mortality: Some animals die as a function of sex, age and disease status (
Population.die()) - Plot
- Subdivide map into discrete units
- Local mortality: additional deaths as a function of local carrying capacity
- Reproduction (babies are born):
Population.reproduce() - Plot
- Advance Time (animals age)
- Diminish Infectious Material in Soil
- Soil Plot
Finish the above, the combine into a single command allowing the model to run for an arbitrary number of iterations (with or without plots being output along the way). Initialize data summary tables and track:
- Demographics
- Disease Prevalence
- Soil Matrices