Include support for phylodynamic analysis

[aezarebski]

Is your feature request related to a problem? Please describe.

I would like to be able to use covasim to simulate datasets for phylodynamic inference.

Describe the solution you'd like

It would be good to have a testing style intervention which generated a tree object encoding the reconstructed tree which could then be fed into software such as BEASTx. I have a working implementation of a solution here but am not sure if there is a better way to do this.

Describe alternatives you've considered

Searching for relevant terms in the repository did not lead me to any part of the code that implements this functionality.

Additional context

See the viral phylodynamics wikipedia page for an introduction. For examples of how this is relevent to the ongoing pandemic one might look to the pango network

[cliffckerr]

Thanks for your suggestion @aezarebski, and fantastic work in your notebook! One of our researchers, @rnunez-IDM , has implemented a version of this to output a sampled transmission tree. However, that tree would still need some type of sequence or similar information that can be used to build a distance metric in a phylogenetic tree. We agree this would be a useful feature to have and would be keen to work with you on implementing something! You can email us at covasim@idmod.org if you want to discuss more details.