\item{file}{a file name specified by either a variable of mode character,
or a double-quoted string.}
\item{tree.names}{if there are several trees to be read, a vector of
- mode character that gives names to the individual trees; if
- \code{NULL} (the default), the trees are named \code{"tree1"},
- \code{"tree2"}, ...}
+ mode character that gives names to the individual trees.}
}
\description{
This function reads one or several trees in a NEXUS file.
}
\details{
The present implementation tries to follow as much as possible the
- NEXUS standard. Only the block ``TREES'' is read; the other data can be
- read with other functions (e.g., \code{\link{read.dna}},
+ NEXUS standard (but see the restriction below on TRANSLATION
+ tables). Only the block ``TREES'' is read; the other data can be read
+ with other functions (e.g., \code{\link{read.dna}},
\code{\link[utils]{read.table}}, ...). A trace of the original data is
kept with the attribute \code{"origin"} (see below).
+ If a TRANSLATION table is present it is assumed that only the tip
+ labels are translated and they are all translated with integers
+ without gap. Consequently, if nodes have labels in the tree(s) they
+ are read as they are and not looked for in the translation table. The
+ logic behind this is that in the vast majority of cases, node labels
+ will be support values rather than proper taxa names. This is
+ consistent with \code{\link{write.nexus}} which translates only the
+ tip labels.
+
`read.nexus' tries to represent correctly trees with a badly
represented root edge (i.e. with an extra pair of parentheses). For
instance, the tree "((A:1,B:1):10);" will be read like "(A:1,B:1):10;"
If several trees are read in the file, the returned object is of class
\code{"multiPhylo"}, and is a list of objects of class \code{"phylo"}.
-
- An attribute \code{"origin"} is further given to the returned object
- which gives the name of the source file (with its path). This is used
- to write a tree in a NEXUS file where all the original data must be
- written (not only the tree) in accordance to the specifications of
- Maddison et al. (1997).
}
\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{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{read.tree}}, \code{\link{write.nexus}},
\code{\link{write.tree}}, \code{\link{read.nexus.data}},