Modular population structure

[GJHSimmons]

Description

A population object should recursively consist of:

• a list S of population objects
• a list V of variables
• a list P of parameters
• a list E of expressions (equations) describing interactions among variables V in terms of parameters P.

The most basic population object consists of:

• S = [self]
• V = [self.variable]
• P = []
• E = []

A population object should provide functionality to assign parameters and expressions to self. Convenience functions should be provided to implement common functionality.

[GJHSimmons]

Population objects have been implemented as described, along with some convenience functions.

For example, the function add_growth_rate(r) creates a parameter growth_rate with value r, and an expression corresponding to the ODE dx/dt = rx. It assigns these to the lists P and E, respectively.

Another convenience function is link_populations. At base, given two populations Pop_1 and Pop_2 with variables x and y, Pop_1 is assigned a parameter flow with value k, and an expression corresponding to the ODE dx/dt = -kx. Pop_2 is also assigned the flow parameter with value k, and an expression corresponding to the ODE dy/dt = kx. The function link_populations takes a subset T of S and a list R of rates, and sequentially links the populations in T with the rates in R according to the above process.

When a population object Pop_1 is added to another population object Pop_2, the lists V,P,E of Pop_2 are updated with the lists V,P,E of Pop_1. Therefore both Pop_1 and Pop_2 describe the full behaviour of Pop_1, however, Pop_2 can obtain additional information, such as interactions of elements of Pop_1 with elements of Pop_2 \ Pop_1.