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Tutorials on phylogenetic and phylogenomic inference
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How to calculate standard deviation base on 95% HPD interval? #11

Closed xiekunwhy closed 3 years ago

xiekunwhy commented 3 years ago

Hi,

In tutorial, you said that "the divergence of Astatotilapia burtoni ("astbur") and the Neolamprologus species was estimated at 6.2666 Ma with a 95% HPD interval from 4.8225 to 7.9049 Ma (...). We can approximate this mean and confidence interval with a lognormal distribution centered at 6.2666 Ma that has a standard deviation (in real space) of 0.13". Can you explain the details of how to approximate the standard deviation based on the known informations?

Best, Kun

mmatschiner commented 3 years ago

Hi, this approximation is not very sophisticated. A practical approach is to plot the distribution in R or in the Prior panel in BEAUti, and to change the standard deviation until you find a value that brings the 2.5% quantile and the 97.5% quantiles of this (lognormal) distribution close to the boundaries of the previously estimated 95% HPD interval. Cheers, Michael

xiekunwhy commented 3 years ago

Hi,

Thank you for your answers, and I will try BEAUti.

Best, kun