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phytools (version 0.3-72.1)

drop.tip.simmap: 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.

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.

See Also

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