drop.dummy.mb: Remove dummy tip from Mr. Bayes summary trees, accounting for...

In EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

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 NULL (default), the tree is simply returned.
dummy.name	name of the added dummy tip, default dummy.
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"))

EvoPhylo documentation built on Nov. 4, 2022, 1:06 a.m.