Description Usage Arguments Details Value Note Author(s) See Also
readNexus
reads a Nexus file and outputs a phylo4
or
phylo4d
or data.frame
object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | readNCL(file, simplify = FALSE, type = c("all", "tree", "data"),
char.all = FALSE, polymorphic.convert = TRUE, levels.uniform = FALSE,
quiet = TRUE, check.node.labels = c("keep", "drop", "asdata"),
return.labels = TRUE, file.format = c("nexus", "newick"),
check.names = TRUE, convert.edge.length = FALSE, ...)
readNexus(file, simplify = FALSE, type = c("all", "tree", "data"),
char.all = FALSE, polymorphic.convert = TRUE, levels.uniform = FALSE,
quiet = TRUE, check.node.labels = c("keep", "drop", "asdata"),
return.labels = TRUE, check.names = TRUE, convert.edge.length = FALSE,
...)
readNewick(file, simplify = FALSE, quiet = TRUE,
check.node.labels = c("keep", "drop", "asdata"),
convert.edge.length = FALSE, ...)
|
file |
a Nexus file for |
simplify |
If there are multiple trees in the file, only the first one is returned if TRUE and a list of phylo4/phylo4d objects is returned if the file contains multiple trees. |
type |
Determines which type of objects to return, if present in the file (see Details). |
char.all |
If TRUE, returns all characters, even those excluded in the NEXUS file |
polymorphic.convert |
If TRUE, converts polymorphic characters to missing data |
levels.uniform |
If TRUE, uses the same levels for all characters |
quiet |
If FALSE the output of the NCL interface is printed. This is mainly for debugging purposes. This option can considerably slow down the process if the tree is big or there are many trees in the file. |
check.node.labels |
Determines how the node labels in the Nexus or Newick files should be treated in the phylo4 object, see Details for more information. |
return.labels |
Determines whether state names (if TRUE) or state codes should be returned. |
file.format |
character indicating the format of the
specified file (either “ |
check.names |
logical. If ‘TRUE’ then the names of the characters from the NEXUS file are checked to ensure that they are syntactically valid variable names and are not duplicated. If necessary they are adjusted (by ‘make.names’) so that they are. |
convert.edge.length |
logical. If ‘TRUE’ negative edge
lengths are replaced with 0. At this time |
... |
Additional arguments to be passed to phylo4 or phylo4d constructor (see Details) |
readNewick
reads a Newick file and outputs a phylo4
or phylo4d
object.
readNexus
extracts data held in a Nexus file, specifically
from DATA, CHARACTER or TREES blocks present in the file. The
type
argument specifies which of these is returned:
will only return a data.frame
of the
contents of all DATA and CHARACTER blocks.
will only
return a phylo4
object of the contents of the TREES block.
if only data or a tree are present in the file, this
option will act as the options above, returning either a
data.frame
or a phylo4
object respectively. If both
are present then a phylo4d
object is returned containing
both.
The function returns NULL
if the type
of
data requested is not present in the file, or if neither data nor
tree blocks are present.
Depending on the context readNexus
will call either the
phylo4
or phylo4d
constructor. In addition with
type="all"
, the phylo4d
constructor will be used if
check.node.labels="asdata"
.
readNewick
imports newick formatted tree files and will
return a phylo4
or a phylo4d
object if the option
check.node.labels="asdata"
is invoked.
For both readNexus
and readNewick
, the options for
check.node.labels
can take the values:
the node labels of the trees will be passed as node
labels in the phylo4
object
the node labels of
the trees will be ignored in the phylo4
object
the node labels will be passed as data and a
phylo4d
object will be returned.
If you use the option
asdata
on a file with no node labels, a warning message is
issued, and thus check.node.labels
takes the value
drop
.
For both readNexus
and readNewick
, additional
arguments can be passed to the constructors such as annote
,
missing.data
or extra.data
. See the documentation of
phylo4-methods, phylo4d and formatData for
the complete list of options.
Depending on the value of type
and the contents of
the file, one of: a data.frame
, a phylo4
object, a phylo4d object or NULL
. If several
trees are included in the Nexus file and the option
simplify=FALSE
a list of phylo4 or
phylo4d objects is returned.
Underscores in state labels (i.e. trait or taxon names) will
be translated to spaces when read by NCL. Unless
check.names=FALSE
, trait names will be converted to valid R
names (see make.names
) on input to R, so spaces will
be translated to periods.
Brian O'Meara, Francois Michonneau, Derrick Zwickl
the phylo4d class, the phylo4 class
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