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epiverse-trace / epichains

[Under active development] Methods for simulating and analysing the sizes and lengths of infectious disease transmission chains from branching process models
https://epiverse-trace.github.io/epichains/
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Likelihood for multi-type clusters #15

Open adamkucharski opened 1 year ago

adamkucharski commented 1 year ago

It's also possible to define a likelihood for multi-type branching process for age-stratified data (Kucharski et al, PLOS Comp Biol, 2015, which is particularly relevant if the population introducing the infection is very different to that driving human-to-human transmission (e.g. older individuals more likely to be index cases for MERS-CoV).

There's a (not particularly tidy) implementation here: https://github.com/adamkucharski/subcritical_chains, which could also be combined with socialmixr.

If multi-type inference not a priority, it may be worth considering a multi-type simulation process for age-stratified social mixing data in meantime (currently implemented as simulate.data() in above repo.

sbfnk commented 1 year ago

That is a nice idea if a fairly substantial extension - would require some thinking about the best user interface.