User:Carl Boettiger/Notebook/Stochastic Population Dynamics/2010/05/29

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Individual based simulation with gamma waiting times

Began implementing the individual-based simulation of gamma waiting times by subdividing the first three age classes into K subclasses. Required rewriting gillespie function so as to intelligently calculate rates rather than writing 3K+1 functions. This leads to an alternative gillespie simulation interface that takes a function to calculate rates, producing cumulative sum (though perhaps that step should be moved into the raw gillespie code) of rates for each event, and an outcome function that will execute the outcome of each of those events. Additionally there is still the fixed interval tasks function and a custom record class for the output.

See the github page for code, commit details, etc.