EvoPhylo (version 0.3.5)

drop.dummy.beast: Remove dummy tip from beast summary trees, accounting for metadata on the tips

Description

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).

Usage

drop.dummy.beast(
  tree.file,
  output.file = NULL,
  dummy.name = "dummy",
  convert.heights = TRUE
)

Value

list of tree converted tree (as treedata) ; and offset age of the youngest tip in the final tree

Arguments

tree.file

path to file containing the tree with dummy tip

output.file

path to file to write converted tree. If NULL (default), the tree is simply returned.

dummy.name

name of the added dummy tip, default dummy.

convert.heights

whether height metadata should be converted to height - offset (required to plot e.g. HPD intervals correctly). Default TRUE.

See Also

drop.dummy.mb() for the same function using summary trees with a "dummy" extant from Mr. Bayes

Examples

# 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"))