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BEAST2-Dev / bdsky

Birth Death Serial Skyline Model for BEAST2
GNU General Public License v3.0
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BDSKY_contemptreeScaler.t:$(n) in BDSKY_contemp.xml and BDSKY_multiRho.xml #25

Closed rbouckaert closed 5 years ago

rbouckaert commented 5 years ago

Greetings from Taming the BEAST down under. This duplication in names causes the scale operator to be incorporated or not at random when the BDSKY_contemp prior is chosen, thus causing problems with the skyline tutorial (https://taming-the-beast.org/tutorials/Skyline-plots/). There are probably other operators that cause problems, so better check the uniqueness of operator names in these templates.

denisekuehnert commented 5 years ago

Thanks, fixed in new release v1.4.4.

tgvaughan commented 5 years ago

For some reason that I can't understand, this realease breaks the Setting Priors TTB tutorial. It is no longer possible to load in the existing Homochronous.xml, add a tMRCA prior on the root, and export it successfully, as doing this results in a number of parameters being removed from the <state> block.

I've tried redoing the tutorial from scratch with the new BDSKY release to generate new XMLs, and the same problem occurs. The problem does not occur with v1.4.3.

Here is the exported from BEAUti before the modification: Homochronous.xml.txt.

Here is the file exported from BEAUti after the addition of the tMRCA prior: Homochronous_tMRCA.xml.txt.

Here is the file generated by loading in Homochronous.xml, adding the tMRCA, then exporting Homochronous_tMRCA_broken.xml.txt.

Any help would be hugely appreciated!

denisekuehnert commented 5 years ago

Looks like i missed some IDs that were still duplicates. Should be fixed now with the new TreePriorsBDSKY template.

tgvaughan commented 5 years ago

Thanks Denise!