some news for ape 3.0-8

[ape.git] / man / read.nexus.Rd

diff --git a/man/read.nexus.Rd b/man/read.nexus.Rd
index d12f4d29f019ef3cb859a202bfb301058e2847ec..5594e0e21c424f33b98ccb29031120aaaed75197 100644 (file)
--- a/man/read.nexus.Rd
+++ b/man/read.nexus.Rd
@@ -8,19 +8,27 @@ read.nexus(file, tree.names = NULL)
   \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 giving names to the individual trees (by default,
+    this uses the labels in the NEXUS file if these are present).}
 }
 \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}},
-  \code{\link[base]{read.table}}, ...). A trace of the original data is
-  kept with the attribute \code{"origin"} (see below).
+  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}}, \dots).
+
+  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
@@ -31,40 +39,14 @@ read.nexus(file, tree.names = NULL)
   message is issued.
 }
 \value{
-  an object of class \code{"phylo"} with the following components:
-  \item{edge}{a two-column matrix of mode character where each row
-    represents an edge of the tree; the nodes and the tips are
-    symbolized with numbers (these numbers are not treated as numeric,
-    hence the mode character); the nodes are represented with negative
-    numbers (the root being \code{"-1"}), and the tips are represented with
-    positive numbers. For each row, the first column gives the
-    ancestor. This representation allows an easy manipulation of the
-    tree, particularly if it is rooted.}
-  \item{edge.length}{a numeric vector giving the lengths of the
-    branches given by \code{edge}.}
-  \item{tip.label}{a vector of mode character giving the names of the
-    tips; the order of the names in this vector corresponds to the
-    (positive) number in \code{edge}.}
-  \item{node.label}{(optional) a vector of mode character giving the
-    names of the nodes (set to \code{NULL} if not available in the file).}
-  \item{root.edge}{(optional) a numeric value giving the length of the
-    branch at the root is it exists (\code{NULL} otherwise).}
-
-  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).
+  an object of class \code{"phylo"} or of class \code{"multiPhylo"}.
 }
 \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}},