1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
|
\name{add.species.to.genus}
\alias{add.species.to.genus}
\alias{genus.to.species.tree}
\title{Add species to genus on a phylogeny or bind simulated species subtrees to a backbone genus tree}
\usage{
add.species.to.genus(tree, species, genus=NULL, where=c("root","random"))
genus.to.species.tree(tree, species)
}
\arguments{
\item{tree}{an object of class \code{"phylo"}. In the case of \code{genus.to.species.tree} this should be a genus-level backbone tree.}
\item{species}{string contain species name in the format \code{"Genus_species"} or \code{"Genus species"}.}
\item{genus}{for \code{add.species.to.genus}, optional argument containing the genus to which \code{species} is to be attached. If \code{NULL} then \code{genus} will be extracted from \code{species}.}
\item{where}{for \code{add.species.to.genus}, the location to attach \code{species} to the tree. \code{where=} \code{"root"} will cause the species to be attached to the MRCA of all members of \code{genus}. \code{where="random"} will cause \code{species} to be attached at random to the subtree descended from the MRCA of all members of \code{genus}.}
}
\description{
\code{add.species.to.genus} adds an additional species to a genus on a phylogeny. \code{genus.to.species.tree} simulates pure-birth subtrees and then binds them at a random height along the terminal edge leading to each corresponding genus on a genus-level backbone tree.
}
\details{
For \code{add.species.to.genus}, if \code{genus} contains only one species and \code{where="root"}, then \code{species} will be attached midway along the branch leading to the one species. If \code{where="random"} then \code{species} will be added at a random position along the edge. If \code{genus} cannot be found in the tree, then the original tree is returned and a warning printed. If the tree is not ultrametric, then the resultant tree may not contain branch lengths and a warning will be printed. If \code{genus} is non-monophyletic then \code{species} will be attached to the most inclusive group containing members of \code{genus} and a warning will be printed.
}
\value{
An object of class \code{"phylo"}.
}
\references{
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
\code{\link{add.random}}, \code{\link{bind.tip}}
}
\keyword{phylogenetics}
\keyword{utilities}
|
