read.nexus(file, tree.names = NULL)
"phylo"
with the following components:"-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.edge
.edge
.NULL
if not available in the file).NULL
otherwise)."multiPhylo"
, and is a list of objects of class "phylo"
. An attribute "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).
read.dna
,
read.table
, ...). A trace of the original data is
kept with the attribute "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 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;" but a warning message will be issued in the former case as this is apparently not a valid Newick format. If there are two root edges (e.g., "(((A:1,B:1):10):10);"), then the tree is not read and an error message is issued.
read.tree
, write.nexus
,
write.tree
, read.nexus.data
,
write.nexus.data