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
|
\name{writeAncestors}
\alias{writeAncestors}
\title{Write a tree to file with ancestral states and (optionally) CIs at nodes}
\usage{
writeAncestors(tree, Anc=NULL, file="", digits=6, format=c("phylip","nexus"),
...)
}
\arguments{
\item{tree}{a phylogenetic tree or set of trees as an object of class \code{"phylo"} or \code{"multiPhylo"}.}
\item{Anc}{a vector of ancestral states, a list containing the ancestral states and 95-percent confidence intervals (as from \code{\link{fastAnc}} or \code{\link{ace}}, or a list of such results.}
\item{file}{an optional string with the filename for output.}
\item{digits}{an integer indicating the number of digits to print for branch lengths and ancestral character values.}
\item{format}{a string indicating whether to output the result in simple Newick (i.e., \code{"phylip"}) or Nexus format.}
\item{...}{additional arguments including \code{x}: a vector of character values, in which case ancestral states are estimated internally using \code{fastAnc}; and \code{CI}: a logical value indicating whether or not to estimate 95-percent confidence intervals.}
}
\description{
This function writes a tree to file with ancestral character states and (optionally) 95-percent confidence intervals stored as node value..
}
\references{
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
}
\value{
A file, string, or vector of strings.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\seealso{
\code{\link{ace}}, \code{\link{fastAnc}}, \code{\link{write.tree}}
}
\keyword{phylogenetics}
\keyword{comparative method}
\keyword{input/output}
|
