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Migrate Ancestral States and Markov Jumps to TreeDataLikelihood #1059

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rambaut opened this issue May 17, 2019 · 1 comment
Open

Migrate Ancestral States and Markov Jumps to TreeDataLikelihood #1059

rambaut opened this issue May 17, 2019 · 1 comment

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@rambaut
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rambaut commented May 17, 2019

Currently AncestralStateBeagleTreeLikelihood and MarkovJumpsBeagleTreeLikelihood are in dr.evomodel.treelikelihood. We should think about how to migrate these abilities to treedatalikelihood (as plugins of some sort to extract realisations at logging).

@ISskandaR
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Hi dears,
I'm facing an issue which log file seems related to the AncestralStateBeagleTreeLikelihood , actually I'm trying to perform a phyolgeographic analysis with discrete traits according to < https://beast.community/workshop_discrete_diffusion > by accomodating dates and locations travels according to (https://beast.community/travel_history.html). I customized the XML file according to each step described in link and I used the customized Beast version available at https://beast.community/tutorials/travel_history/files/beast_travel_history.jar .
Unfortunately even by strictly following the format in the sample XML at https://beast.community/tutorials/travel_history/files/9seqs_travelHistory.xml (taking in account any differences in between the inputs ) I did not succeed ; after my best try I got the following message :

LOG

I'd appreciate any kind of support
Best regards

@rambaut rambaut added this to the v1.11 milestone Aug 15, 2023
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