Question: Confidence interval missing problem

[Guo Yuelong]

Dear all,

I have a question about the 95% confidence interval given at the end
of analysis.
I run a BEAST program to date the ancestral node divergence time, with
the relaxed molecular clock models selected. Two priors, with normal
distribution, was set to two of my basal nodes. The analysis was
finished successfully without any error message. However, when I was
trying to show the error bar on the tree using FigTree, half of error
bars does not show up, while the other half shown seemingly correct on
the tree. Same thing happened if I choose to show the 95% confidence
interval in form of numbers on each node. Does anyone have any idea
why this happened?
Thanks for your attention and your help.

Sincerely,
Yuelong

[Eugenio Valderrama]

Dear Yuelong,

Actually I have the same problem, did you solve it already?
If you did it I would be very grateful if you share the solution.

Best regards,

Eugenio Valderrama

[julien]

Hi !

Just a guess... I am not sure at all...

However, I remember how surprised I was while discovering first Beast
results... Indeed, very often the 95%HPD bar was next to nodes,
without spanning the node value itself (not for all nodes however)...

Might it be the problem ? However it is difficult to see from
overseas :-)

In my case, it was just because I selected in Treeannotator the option
"keep target height". As confidence intervals are calculated from all
trees, sometimes node heights in the target tree can "fall" outside
95% HPD...

Hope that helps !

Julien

[Julian Dupuis]

Hi again,

With some more digging I answered my own question. In case anyone else has experienced the same problem, you simply have to set the posterior probability limit to 0 in treeannotator.

Sorry for the unnecessary post.

Julian

On 2013-06-08, at 12:16 PM, Julian Dupuis <jrdu...@ualberta.ca> wrote:

Hello All,

I'm having the same problem as below. Does anyone have any thoughts?

Thank you,

Julian

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