drop.tip.simmap: Drop tips or extract clade from tree with mapped discrete...

View source: R/drop.tip.simmap.R

drop.tip.simmapR Documentation

Drop tips or extract clade from tree with mapped discrete character

Description

This function drops one or multiple tips from the modified "phylo" object with a mapped binary or multistate trait (see read.simmap) while maintaining the matrix $mapped.edge and list of mappings by branch maps. This function is equivalent to drop.tip but for a tree with a mapped discrete character.

extract.clade.simmap is functionally equivalent to extract.clade but preserves discrete character mappings on the tree.

Usage

drop.tip.simmap(tree, tip, ...)
extract.clade.simmap(tree, node)

Arguments

tree

a modified object of class "phylo" (see read.simmap).

tip

name or names of species to be dropped.

node

node number for the root node of the clade to be extracted.

...

optional arguments. Currently the logical argument untangle which if set to TRUE will call untangle before returning the "simmap" object to the user.

Value

A modified object of class "phylo" containing the elements maps and $mapped.edge with the time spent in each state along each edge of the tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

See Also

brownie.lite, drop.tip, extract.clade, make.simmap, read.simmap, sim.history


phytools documentation built on Sept. 2, 2022, 1:06 a.m.