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ropensci / babette

babette is an R package to work with BEAST2
https://docs.ropensci.org/babette
GNU General Public License v3.0
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How to prepare a tipdating file? #91

Closed richelbilderbeek closed 3 years ago

richelbilderbeek commented 4 years ago

Email from Naira Dekhil Ben Attia:

I would like to use babette for genome dating and phylogeography. I didin't inderstand how we could prepare a tipdates file including yy/mm/dd. Is there any recommendation.

richelbilderbeek commented 4 years ago

An example can be found here:

Note that tipdating is still an experimental feature. If you find a bug, you are encouraged to share it with me!

richelbilderbeek commented 4 years ago

I would like to inform you that my tipdates file contains year, month and day. In this issue only year is montioned. So, could you help us how to perform.

richelbilderbeek commented 4 years ago

So, could you help us how to perform.

I have no idea how to create a proper tipdates file: some babette users simply submit them. I -like you- would just try until it works. An alternative is to use BEAUti (part of BEAST2) to test out your file without coding.

richelbilderbeek commented 4 years ago

I have tried with your recommendation for tipdates file and I have obtained this error only with relax clock model: Error in check_input_filename_validity(input_filename = bifs$input_filename_full, : 'input_filename' must be a valid BEAST2 XML file.

richelbilderbeek commented 4 years ago

Looks like the error is on my side, probably similar to #90.

richelbilderbeek commented 4 years ago

Hi Niara.

It appears the error is on babette's side as it is similar to another reported tipdating bug [1]: the file created to run BEAST2 with is simply invalid.

As I said: tipdating is an experimental feature!

If you want to encourage me to fix it, I will need a reprex [2], which is some code and your tipdates filename.

Another option is to use BEAST2 directly, with the GUI program called BEAUti.

I hope that helps, Richel Bilderbeek

  [1] https://github.com/ropensci/babette/issues/90   [2] https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html\

richelbilderbeek commented 3 years ago

Closing this Issue, as there is no reply :+1: