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thibautjombart / treescape

Exploring tree diversity
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Add BEAST dataset #46

Open thibautjombart opened 9 years ago

thibautjombart commented 9 years ago

From one of the well-known practicals. We basically just need to posterior sample of trees

MichelleKendall commented 9 years ago

I have four sets of BEAST trees (with four different sets of priors) for dengue fever, built from the xmls supplied in the original BEAST paper http://www.biomedcentral.com/1471-2148/7/214/additional

Is that the sort of thing you're thinking of?

thibautjombart commented 9 years ago

Yes absolutely! I have added a HA H3N2 dataset they used in a tutorial at 5167cf2c911b099066c45cc4288a89484910f375 (this is on branch newfeatures)

BTW, data can be documented using roxygen2 too. I made that change - see https://github.com/thibautjombart/treescape/blob/newfeatures/R/data.R

MichelleKendall commented 8 years ago

Sorry I completely forgot this was on branch newfeatures. I've now included the flu trees and proper documentation in the master branch, along with the Dengue trees as promised. I haven't put the flu trees as an automatic example in Shiny because they're quite big and a bit slow, but they're a great example to include in the package, thanks.

You said you used the first 200 trees from the BEAST run - did you already discard some trees as a burn-in? It usually makes more sense to use the final 200 or a random sample of 200 from the second half, was there a reason not to do that here? Thanks.