Hi all,
What is the best way to incorporate travel history in the discrete phylogeographic analysis?
Is it just a matter of, for example, using the country_exposure column (and other exposure columns) as geographic information, or is there a specific command used for travel information to be taken into account?
Thank you,
Anderson
Hi Anderson!
It would be good if some others from the team could chime in to ensure I’ve got this straight, but I believe that just using the country_exposure column and then passing this into augur traits should do the trick - this is what we do in our Nextstrain.org ncov builds. We then do some fiddling afterwards to try and align this with the display… see incorporate_travel_history rule (and corresponding script) here. This is some adjustment so that the nodes show up the color of the place they were sampled, with the exposure location being a separate trait - but this isn’t necessary if you’re just interested in using the exposure information to infer traits on internal nodes and are less concerned for appearances!
I hope that helps!