trying to set-up a xml for sars-cov-2 (december january)

[babarlelephant]

Hi,

• I'm a bit lost on the parameters, particularly mu and nu that appear to be critical.

  The clockrate is fixed to 0.0008/subs/site/year

• 155 sequences from December 2019 and January 2020 and the epidemic curve from https://github.com/chaolongwang/SAPHIRE/blob/master/data/Covid19CasesWH.csv

• The goal is to see how it affects the tMRCA

• My xml is there https://github.com/babarlelephant/trash/blob/main/consensus-155.xml (the one with the sequences is in the same repo)

• When letting the uniform prior [0,1] on nu the tMRCA converges to roughly the origin time (late October) but my epidemic curve has 0 cases until December 8.

• When setting lower=0.5 for nu it converges to a much more recent date.

  There is a short description of the parameters in https://github.com/aezarebski/timtam2/blob/main/src/timtam/TimTam.java

Thanks a lot!

[aezarebski]

Hi @babarlelephant,

Thanks for getting in touch and trying to use the package; as I'm sure you've noticed, the documentation is a work in progress.

Yes, it makes sense that setting nu=0.5 would lead to a more recent date if the time series has a bunch of zeros at the start. A couple of options would be to either: cut the start of the time series off, or use a time varying observation probability to allow for changes in the observation system as the outbreak was recognised.

I haven't had a chance to look through your XML carefully, but it looks like you are using years as your unit of time in which case the "removal" rate mu=0.146 is a bit low. Also, I'm a little confused about how you are handling the origin. I think it should be originTime=@origin.t.

Please let me know how you get along, I'll leave this issue open in the meantime.

Cheers, Alex