trying to set-up a xml for sars-cov-2 (december january)
Created by: 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
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155 sequences from December 2019 and January 2020 and the epidemic curve from https://github.com/chaolongwang/SAPHIRE/blob/master/data/Covid19CasesWH.csv
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The goal is to see how it affects the tMRCA
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My xml is there https://github.com/babarlelephant/trash/blob/main/consensus-155.xml (the one with the sequences is in the same repo)
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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.
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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!