Flu vaccine distances about augur HOT 4 CLOSED

Ahh, yes. Can do. I'll finish writing hour and then start on that later this afternoon.

Ehh, the seasonal binning is delicate enough I'd rather do it downstream where there are fewer moving parts and I can clearly see what's happening / breaking.

from augur.

Sure, I'd be happy to. But, as you noted in your email,

Antigenic distance...should be the average of tips in a clade that are circulating in a given season

Thus, these values of "antigenic distance" are actually time-dependent.
E.g., let's say clade A has 10 descendants in the tree. 3 of these tips are from 2014-2015, while 7 are from 2015-2016. The mean antigenic distance for 2014-2015 clade A descendants to vaccine will be different than the mean antigenic distance for 2015-2016 clade A descendants vs. vaccine.

from augur.

Yes. Antigenic distances between vaccine strains and clades will be time-dependent. Here, I was thinking to just output antigenic distances between vaccine strains and individual tips. These pairwise measurements do not suffer from time dependence. Binning into seasons, etc... can happen downstream.

Although... the other approach would be to do that seasonal binning here. Fairly agnostic on this point.

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This issue was resolved by PR #101.

from augur.