TreeTools (version 2.4.1)

ReadCharacters: Read phylogenetic characters from file

Description

Parse a Nexus Maddison1997TreeTools or TNT Goloboff2008TreeTools file, reading character states and names.

Usage

ReadCharacters(filepath, character_num = NULL, encoding = "UTF8")
ReadTntCharacters(
  filepath,
  character_num = NULL,
  type = NULL,
  encoding = "UTF8"
)
ReadTNTCharacters(
  filepath,
  character_num = NULL,
  type = NULL,
  encoding = "UTF8"
)
ReadNotes(filepath, encoding = "UTF8")
ReadAsPhyDat(...)
ReadTntAsPhyDat(...)
ReadTNTAsPhyDat(...)
PhyDat(dataset)

Value

ReadCharacters() and ReadTNTCharacters() return a matrix whose row names correspond to tip labels, and column names correspond to character labels, with the attribute state.labels listing the state labels for each character; or a list of length one containing a character string explaining why the function call was unsuccessful.

ReadAsPhyDat() and ReadTntAsPhyDat() return a phyDat object.

ReadTntCharacters() and ReadTNTCharacters() return a matrix as described above for ReadCharacters(). When the TNT file contains an xgroup partition block Goloboff2008TreeTools, the returned matrix carries an "xgroup" attribute: a factor of length ncol(matrix)

whose levels are the partition labels (the parenthetical label, e.g.\ "ANTERIOR", or the numeric id as a string when no label is given). Characters not assigned to any partition are NA. The attribute is absent (not an all-NA vector) when no xgroup block is found in the file.

ReadNotes() returns a list in which each entry corresponds to a single character, and itself contains a list of with two elements:

1. A single character object listing any notes associated with the character

2. A named character vector listing the notes associated with each taxon for that character, named with the names of each note-bearing taxon.

Arguments

filepath

character string specifying location of file, or a connection to the file.

character_num

Index of character(s) to return. NULL, the default, returns all characters.

encoding

Character encoding of input file.

type

Character vector specifying categories of data to extract from file. Setting type = c("num", "dna") will return only characters following a &[num] or &[dna] tag in a TNT input file, listing num character blocks before dna characters. Leave as NULL (the default) to return all characters in their original sequence.

...

Parameters to pass to Read[Tnt]Characters().

dataset

list of taxa and characters, in the format produced by read.nexus.data(): a list of sequences each made of a single character vector, and named with the taxon name.

Functions

• PhyDat(): A convenient wrapper for phangorn's phyDat(), which converts a list of morphological characters into a phyDat object. If your morphological characters are in the form of a matrix, perhaps because they have been read using read.table(), try MatrixToPhyDat() instead.

Author

Martin R. Smith ()

Details

Tested with matrices downloaded from MorphoBank OLeary2011TreeTools, but should also work more widely; please report incompletely or incorrectly parsed files.

Matrices must contain only continuous or only discrete characters; maximum one matrix per file. Continuous characters will be read as strings (i.e. base type "character").

The encoding of an input file will be automatically determined by R. Errors pertaining to an invalid multibyte string or string invalid at that locale indicate that R has failed to detect the appropriate encoding. Either re-save the file in a supported encoding (UTF-8 is a good choice) or specify the file encoding (which you can find by, for example, opening in Notepad++ and identifying the highlighted option in the "Encoding" menu) following the example below.

References

See Also

• Convert between matrices and phyDat objects: MatrixToPhyDat()

• Write characters to TNT-format file: WriteTntCharacters()

Examples

fileName <- paste0(system.file(package = "TreeTools"),
                   "/extdata/input/dataset.nex")
ReadCharacters(fileName)

fileName <- paste0(system.file(package = "TreeTools"),
                   "/extdata/tests/continuous.nex")

continuous <- ReadCharacters(fileName, encoding = "UTF8")

# To convert from strings to numbers:
at <- attributes(continuous)
continuous <- suppressWarnings(as.numeric(continuous))
attributes(continuous) <- at
continuous
tntFile <- paste0(system.file(package = "TreeTools"),
                  "/extdata/tests/tnt-xgroup.tnt")
mat <- ReadTntCharacters(tntFile)
attr(mat, "xgroup")