offset.to.dummy: Convert trees produced by a BEAST2 FBD analysis with offset...

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

Convert trees produced by a BEAST2 FBD analysis with offset to trees with correct ages.

Description

This method adds a dummy tip at the present (t = 0) to fully extinct trees with offsets, in order to have correct ages (otherwise the most recent tip is assumed to be at 0). This is a workaround to get the proper ages of the trees into other tools such as TreeAnnotator.

Usage

offset.to.dummy(trees.file, log.file, output.file = NULL, dummy.name = "dummy")

Arguments

trees.file	path to BEAST2 output file containing posterior trees
log.file	path to BEAST2 trace log file containing offset values
output.file	path to file to write converted trees. If NULL (default), trees are simply returned.
dummy.name	name of the added dummy tip, default dummy.

Details

NB: Any metadata present on the tips will be discarded. If you want to keep metadata (such as clock rate values), use offset.to.dummy.metadata instead.

Value

list of converted trees (as treedata)

See Also

offset.to.dummy.metadata() (slower version, keeping metadata)

Examples

# Convert trees with offset to trees with dummy tip
trees_file <- system.file("extdata", "ex_offset.trees", package = "EvoPhylo")
log_file <- system.file("extdata", "ex_offset.log", package = "EvoPhylo")
converted_trees <- offset.to.dummy.metadata(trees_file, log_file)

# Do something with the converted trees - 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"))

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