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\name{read.nexus.data}
\alias{read.nexus.data}
\alias{nexus2DNAbin}
\title{
Read Character Data In NEXUS Format
}
\description{
\code{read.nexus.data} reads a file with sequences in the NEXUS
format. \code{nexus2DNAbin} is a helper function to convert the output
from the previous function into the class \code{"DNAbin"}.
For the moment, only sequence data (DNA or protein) are supported.
}
\usage{
read.nexus.data(file)
nexus2DNAbin(x)
}
\arguments{
\item{file}{a file name specified by either a variable of mode
character, or a double-quoted string.}
\item{x}{an object output by \code{read.nexus.data}.}
}
\details{
This parser tries to read data from a file written in a
\emph{restricted} NEXUS format (see examples below).
Please see files \file{data.nex} and \file{taxacharacters.nex} for
examples of formats that will work.
Some noticeable exceptions from the NEXUS standard (non-exhaustive
list):
\itemize{
\item{\bold{I}}{Comments must be either on separate lines or at the
end of lines. Examples:\cr
\code{[Comment]} \bold{--- OK}\cr
\code{Taxon ACGTACG [Comment]} \bold{--- OK}\cr
\code{[Comment line 1}
\code{Comment line 2]} \bold{--- NOT OK!}\cr
\code{Tax[Comment]on ACG[Comment]T} \bold{--- NOT OK!}}
\item{\bold{II}}{No spaces (or comments) are allowed in the
sequences. Examples:\cr
\code{name ACGT} \bold{--- OK}\cr
\code{name AC GT} \bold{--- NOT OK!}}
\item{\bold{III}}{No spaces are allowed in taxon names, not even if
names are in single quotes. That is, single-quoted names are not
treated as such by the parser. Examples:\cr
\code{Genus_species} \bold{--- OK}\cr
\code{'Genus_species'} \bold{--- OK}\cr
\code{'Genus species'} \bold{--- NOT OK!}}
\item{\bold{IV}}{The trailing \code{end} that closes the
\code{matrix} must be on a separate line. Examples:\cr
\code{taxon AACCGGT}
\code{end;} \bold{--- OK}\cr
\code{taxon AACCGGT;}
\code{end;} \bold{--- OK}\cr
\code{taxon AACCCGT; end;} \bold{--- NOT OK!}}
\item{\bold{V}}{Multistate characters are not allowed. That is,
NEXUS allows you to specify multiple character states at a
character position either as an uncertainty, \code{(XY)}, or as an
actual appearance of multiple states, \code{\{XY\}}. This is
information is not handled by the parser. Examples:\cr
\code{taxon 0011?110} \bold{--- OK}\cr
\code{taxon 0011{01}110} \bold{--- NOT OK!}\cr
\code{taxon 0011(01)110} \bold{--- NOT OK!}}
\item{\bold{VI}}{The number of taxa must be on the same line as
\code{ntax}. The same applies to \code{nchar}. Examples:\cr
\code{ntax = 12} \bold{--- OK}\cr
\code{ntax =}
\code{12} \bold{--- NOT OK!}}
\item{\bold{VII}}{The word \dQuote{matrix} can not occur anywhere in
the file before the actual \code{matrix} command, unless it is in
a comment. Examples:\cr
\code{BEGIN CHARACTERS;}
\code{TITLE 'Data in file "03a-cytochromeB.nex"';}
\code{DIMENSIONS NCHAR=382;}
\code{FORMAT DATATYPE=Protein GAP=- MISSING=?;}
\code{["This is The Matrix"]} \bold{--- OK}
\code{MATRIX}\cr
\code{BEGIN CHARACTERS;}
\code{TITLE 'Matrix in file "03a-cytochromeB.nex"';} \bold{--- NOT OK!}
\code{DIMENSIONS NCHAR=382;}
\code{FORMAT DATATYPE=Protein GAP=- MISSING=?;}
\code{MATRIX}}
}
}
\value{
A list of sequences each made of a single vector of mode character
where each element is a (phylogenetic) character state.
}
\references{
Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an
extensible file format for systematic information. \emph{Systematic
Biology}, \bold{46}, 590--621.
}
\author{Johan Nylander, Thomas Guillerme, and Klaus Schliep}
\seealso{
\code{\link{read.nexus}}, \code{\link{write.nexus}},
\code{\link{write.nexus.data}}
}
\examples{
## Use read.nexus.data to read a file in NEXUS format into object x
\dontrun{x <- read.nexus.data("file.nex")}
}
\keyword{file}
|
