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Resulting xml cannot estimate clock rate in a uniform distribution prior #135
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Hi @pedrotaucce, thanks for this excellent bug report (and sorry for replying so late). I will take a look at it now :-) |
@pedrotaucce will work on this tomorrow :-) |
Thanks! I really appreciate that. I have more than 40 alignments and will have to different beast runs. Your package is being a lifesaver! |
Plan:
|
For completeness, this is the XML generated by BEAUti:
Take special note at ...
... especially the This proves -in a way- that time is normalized to 1.0 |
Here I write down the solution to this Issue: Dear user, Thanks for this excellent bug report. It is clear the problem is (1) you want to estimate a clock rate, (2) the output of BEAST2 does not show an estimated clock rate. This is not a bug in nor I predict you want to, however, get an actual clock rate. The way to do this is simple: if you know the phylogeny is -say- 15 million, then one can multiply/divide things by 15. Another way is to take a known timespan within the phylogeny and rescale based on that:
I hope this answer helps you and future users! I'll close this Issue if you agree or after a month :-) |
Some emails later we've zoomed in on the Issue, with again an awesome bug by @pedrotaucce:
Earlier I misunderstood this. Thanks Pedro for correcting me
BEAUTi:
BEAUTi:
BEAUTi: same as 1, but with MRCA prior
BEAUTi: the same as number 2, but with MRCA prior just like number 3. I ran all the xml files, and numbers 2 and 4 did estimate the clock rate according to the prior:
Nope, please keep sending these awesome bug reports! |
I'll first concentrate on 2. The error is quite clear: this is what
This is what BEAUti gives:
Note the lack of I will reproduce the BEAUti file with the Problem is that setting 1 already fails, so fix that one first :-) |
…ing estimated, progress #135
Describe the bug
I am using the package to run beast in several mitochondrial alignments, it is being really helpful, thanks!
I don't know if I am doing something wrong, but I cannot estimate clock rate using an uniform prior. The xml file produced has 'estimate="false"' on it.
To Reproduce
Script to reproduce the behavior:
Expected behavior
I expected the resulting xml file to make possible to estimate the clock rate based on the uniform prior interval
Screenshots
If applicable, add screenshots to help explain your problem.
Environment:
Show the results of running the following script:
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