drop.tip.simmap

extract.clade.simmap

a modified object of class <code>"phylo"</code> (see <code><a rd-options="" href="/link/read.simmap?package=phytools&version=0.7-70" data-mini-rdoc="phytools::read.simmap">read.simmap</a></code>).

tree

name or names of species to be dropped.

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

node

This function drops one or multiple tips from the modified <code>"phylo"</code> object with a mapped binary or multistate trait (see <code><a rd-options="" href="/link/read.simmap?package=phytools&version=0.7-70" data-mini-rdoc="phytools::read.simmap">read.simmap</a></code>) while maintaining the matrix <code>$mapped.edge</code> and list of mappings by branch <code>maps</code>. This function is equivalent to <code><a rd-options="" href="/link/drop.tip?package=phytools&version=0.7-70" data-mini-rdoc="phytools::drop.tip">drop.tip</a></code> but for a tree with a mapped discrete character.
<code>extract.clade.simmap</code> is functionally equivalent to <code><a rd-options="" href="/link/extract.clade?package=phytools&version=0.7-70" data-mini-rdoc="phytools::extract.clade">extract.clade</a></code> but preserves discrete character mappings on the tree.

utilities

phylogenetics

A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

drop.tip.simmap function

a modified object of class <code>"phylo"</code> (see <code><a rd-options='' href='read.simmap'>read.simmap</a></code>).

This function drops one or multiple tips from the modified <code>"phylo"</code> object with a mapped binary or multistate trait (see <code><a rd-options='' href='read.simmap'>read.simmap</a></code>) while maintaining the matrix <code>$mapped.edge</code> and list of mappings by branch <code>maps</code>. This function is equivalent to <code><a rd-options='' href='drop.tip'>drop.tip</a></code> but for a tree with a mapped discrete character.
<code>extract.clade.simmap</code> is functionally equivalent to <code><a rd-options='' href='extract.clade'>extract.clade</a></code> but preserves discrete character mappings on the tree.

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

Description

Usage

Arguments

Value

References

See Also