Extracting, in tabular format, posterior locations from a discrete phylogeographic analysis

[carlo pacioni]

Hi everyone,?

I have conducted a discrete phylogeographic analysis in BEAST 2.5.1 and would like to extract in a tabular format the posterior probability of the locations of a bunch of tips. I'm sure there must be a R package or some other utilities to extract this info available. Could you please point me to a solution? I know that this statistics is collected by TreeAnnotator and I can visualize it in the MCC tree (or by manually searching the MCC tree file) under the location.set and location.set.prob, but I'm looking for a faster, more automated way to do this.

thanks,

carlo

[Santiago Sánchez]

Hi Carlo,

Check out my R package, rBt, to extract metadata from BEAST annotated trees. I’ve tested it with Beast2 and Beast1 trees, and it also works with MCC and posterior trees.

https://github.com/santiagosnchez/rBt

Example:

library(devtools)
install_github(“santiagosnchez/rBt”)
tre = read.annot.beast(‘mytree.mcc.tre’)
head(tre$metadata)

Let me know if you have questions.

Cheers,
Santiago

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[Carlo Pacioni]

Thanks Santiago,

Exactly what I needed!

Carlo