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reconhub / outbreaker2

Disease outbreak reconstruction from epidemiological and genetic data
http://www.repidemicsconsortium.org/outbreaker2/
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Updated genetic likelihood and kappa tests #54

Closed finlaycampbell closed 5 years ago

finlaycampbell commented 5 years ago

Now includes the correct genetic likelihood, with a description in the README of the changes and derivations of the new likelihood.

I added a test to check kappas are being estimated correctly.

I added small additional features such as an optional progress bar and case-labelling for plot.outbreaker_chains.