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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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Combine discrete traits into one partition? #1161

Closed sanderdebacker closed 1 year ago

sanderdebacker commented 1 year ago

I'm importing a mapping file containing the present (Y) or absent (N) state for each taxon in the data partition across 90 traits. When selecting all discrete traits and creating a partition, it creates one for each trait. I'm used to continuous traits where for example I'm able to combine latitude and longitude (as two different traits) into one partition.

Is this possible for discrete traits?

gabehassler commented 1 year ago

Hi @sanderdebacker, the answer depends on why you want to combine the 90 traits into a single partition. Likely there is a solution that is implemented in BEAST but not available in BEAUti.

The solution will probably involve a combination of a latent liability model to map your discrete traits to a continuous space and a latent factor model for dimension reduction (90 traits is a lot for a joint trait model).

I'm closing this issue because it's not a bug in BEAST, but I'm happy to discuss specifics further on the BEAST users google group (https://groups.google.com/g/beast-users).