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xavierdidelot / BactDating

Bayesian inference of ancestral dates on bacterial phylogenetic trees
https://xavierdidelot.github.io/BactDating
MIT License
80 stars 15 forks source link

pstrict value explanation! #25

Closed nbawe closed 4 years ago

nbawe commented 4 years ago

Hello what is pstrict value and how to interpreted? For example:

res=bactdate(tree,dates,useRec=T)
res$pstrict
## [1] 0

Thank you

xavierdidelot commented 4 years ago

This is the probability that the clock is strict, rather than relaxed. If this value is zero, it means that a relaxed clock is definitely preferred.

nbawe commented 4 years ago

So if I used default res=bactdate(tree,dates,useRec=T) command and by default model is mixedgamma then pstrict indicates relaxed clock - should I rerun analysis with relaxedgamma or mixedgamma already used relaxed model?

xavierdidelot commented 4 years ago

No there is no need to rerun, because pstrict=0 indicates that a strict clock was always rejected and therefore never used. So the output of relaxedgamma would be the same as the output of mixedgamma.

nbawe commented 4 years ago

Thank you - very much.