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harrispopgen / mushi

[mu]tation [s]pectrum [h]istory [i]nference
https://harrispopgen.github.io/mushi/
MIT License
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trapezoidal instead of box quadrature for expected coalescent times #2

Closed wsdewitt closed 5 years ago

wsdewitt commented 5 years ago

We're currently using eqs (2) and (3) from Rosen et al. which are a piecewise constant discretization of the integral of eqn (1). We need to recast this as piecewise linear so we can properly penalize the derivative.

When this is done, also change the plotting code to plt.plot instead of plt.step.

wsdewitt commented 5 years ago

I think it's fine to keep piecewise constant. It saves us a lot of work because we can almost directly borrow the discretization of Rosen et al.