R: Read phylogenetic characters from file

ReadCharacters {TreeTools} | R Documentation

## Read phylogenetic characters from file

### Description

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

### Usage

    ReadCharacters(
      filepath,
      character_num = NULL,
      encoding = "UTF8",
      session = NULL
    )

    ReadTntCharacters(
      filepath,
      character_num = NULL,
      type = NULL,
      session = NULL,
      encoding = "UTF8"
    )

    ReadNotes(filepath, encoding = "UTF8")

    ReadAsPhyDat(...)

    ReadTntAsPhyDat(...)

    PhyDat(dataset)

### 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.
`session` | (Optional) A Shiny session with a `numericInput` named `character_num` whose maximum should be updated.
`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.

### Details

Tested with matrices downloaded from MorphoBank, 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.

### 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.

`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.

### 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(s)

Martin R. Smith (martin.smith@durham.ac.uk)

### References

Maddison DR, Swofford DL, Maddison WP (1997). “Nexus: an extensible file format for systematic information.” Systematic Biology, 46, 590–621. doi: 10.1093/sysbio/46.4.590.

### 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

[Package TreeTools version 1.5.1 Index]