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phylobase (version 0.6.8)

Import Nexus and Newick files: Create a phylo4, phylo4d or data.frame object from a Nexus or a Newick file

Description

readNexus reads a Nexus file and outputs a phylo4 or phylo4d or data.frame object. readNewick reads a Newick file and outputs a phylo4 or phylo4d object.

Usage

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, ...)

Arguments

file
a Nexus file for readNexus or a file that contains Newick formatted trees for readNewick
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.
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
convert.edge.length
logical. If TRUE negative edge lengths are replaced with 0. At this time phylobase does not accept objects with negative branch lengths, this workaround allows to still use trees with negative branch lengths are a
...
Additional arguments to be passed to phylo4 or phylo4d constructor (see Details)

Value

  • 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.

Details

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: [object Object],[object Object],[object Object] 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: [object Object],[object Object],[object Object] 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.

See Also

the phylo4d class, the phylo4 class