drop.tip.simmap {phytools} | R Documentation |
Drop tips or extract clade from tree with mapped discrete character
Description
This function drops one or multiple tips from an object of class "simmap"
.
Usage
## S3 method for class 'simmap'
drop.tip(phy, tip, ...)
## S3 method for class 'simmap'
keep.tip(phy, tip, ...)
extract.clade.simmap(tree, node)
Arguments
phy |
an object of class |
tip |
name or names of species to be dropped (or kept). |
node |
node number for the root node of the clade to be extracted. |
... |
optional arguments. Currently the logical argument |
tree |
for |
Details
Equivalent to drop.tip
and keep.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.
Following drop.tip
in ape, the returned tree is always in "cladewise"
order.
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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
See Also
drop.tip
, extract.clade
, make.simmap
, read.simmap
, sim.history