drop.dummy.mb {EvoPhylo} | R Documentation |
Remove dummy tip from Mr. Bayes summary trees, accounting for metadata on the tips
Description
This method is designed to remove the dummy tip added to a dataset before running with Mr. Bayes.
Usage
drop.dummy.mb(
tree.file,
output.file = NULL,
dummy.name = "dummy",
convert.ages = TRUE
)
Arguments
tree.file |
path to file containing the tree with dummy tip |
output.file |
path to file to write converted tree. If |
dummy.name |
name of the added dummy tip, default |
convert.ages |
whether height metadata should be converted to height - offset (required to plot e.g. HPD intervals correctly). Default TRUE. |
Value
list of tree
converted tree (as treedata) ; and offset
age of the youngest tip in the final tree
See Also
drop.dummy.beast()
for the same function using summary trees with a "dummy" extant from BEAST2
Examples
# Remove the dummy tip from the summary tree
final_tree <- drop.dummy.mb(system.file("extdata", "tree_mb_dummy.tre", package = "EvoPhylo"))
[Package EvoPhylo version 0.3.2 Index]