Tsdate 0.2.1 - Githubissues

hyanwong commented 3 months ago

As someone involved in the recent tsdate releases, I'm wondering how tsinfer+tsdate_v0.2.1 performs (e.g. compared to Relate). The recommended way to perform ARG inference now is

import tsinfer
import tsdate
topology_only_ts = tsinfer.infer(data)
# Use a tsdate version that defaults to the new "variational gamma" method
assert tsdate.__version__.startswith("0.2."). # quick hack to check at least v0.2
ts = tsdate.date(tsdate.preprocess_ts(topology_only_ts), mutation_rate=mu)

dandanpeng commented 3 months ago

Thank you for the information! We'll check this and update our manuscript.

hyanwong commented 3 months ago

Great, thanks. Let me know if you need any extra information.

dandanpeng / ARG_Benchmarking

Tsdate 0.2.1 #2