Remove dummy tip from beast summary trees, accounting for metadata on the tipsSource:
This method is designed to remove the dummy tip added on offset trees once postprocessing is complete (for instance once the summary tree has been built using TreeAnnotator).
drop.dummy.beast( tree.file, output.file = NULL, dummy.name = "dummy", convert.heights = TRUE )
path to file containing the tree with dummy tip
path to file to write converted tree. If
NULL(default), the tree is simply returned.
name of the added dummy tip, default
whether height metadata should be converted to height - offset (required to plot e.g. HPD intervals correctly). Default TRUE.
tree converted tree (as treedata) ; and
offset age of the youngest tip in the final tree
drop.dummy.mb() for the same function using summary trees with a "dummy" extant from Mr. Bayes
# Analyze the trees with dummy tips - for instance, calculate the MCC summary tree # Then remove the dummy tip from the MCC tree final_tree <- drop.dummy.beast(system.file("extdata", "ex_offset.MCC.tre", package = "EvoPhylo"))