Moran Process with Mutation

[marcharper]

I also made some improvements to the Moran process implementation -- it better handles unique player types now by using the string representations of the players. In the previous implementation the process would not have distinguished between Random(0.5) and Random(0.25), for example.

Re #754

[drvinceknight]

Awesome.

1 minor request but could you also add something to the documentation please? In particular showing how it needs to be used as an iterator?

[drvinceknight]

A lot of the literature I've seen write this in a generic way with a matrix $M$ for mutation where $M_ij$ is the probability if mutating from species $i$ to $j$. Is that worth doing (perhaps at a later date)?

More of a question than a request. We could simply have that the mutation rate could either be a float or a 2 d array... (Or whatever: not suggest this needs to be done here).

[marcharper]

Yes, we could do that. This implementation uses the "standard matrix" which is 1 - mu on the diagonal and mu / (n-1) elsewhere with n being the number of types and mu the mutation rate.

In my experience this is far more common than an arbitrary mutation matrix but we can certainly generalize later.

[drvinceknight]

In my experience this is far more common than an arbitrary mutation matrix but we can certainly generalize later.

Yeah no doubt I'm reading theoretic stuff but in general the numeric computations would be using this form. :)

[drvinceknight]

could we make mt: mutation_matrix or similar?

[marcharper]

Sure