R: Extract taxa from a matrix block

ExtractTaxa {TreeTools} | R Documentation

## Extract taxa from a matrix block

### Description

Extract leaf labels and character states from a Nexus-formatted matrix.

### Usage

    ExtractTaxa(
      matrixLines,
      character_num = NULL,
      session = NULL,
      continuous = FALSE
    )

    NexusTokens(tokens, character_num = NULL, session = NULL)

### Arguments

`matrixLines` | Character vector containing lines of a file that include a phylogenetic matrix. See `ReadCharacters()` for expected format.
`character_num` | Index of character(s) to return. `NULL`, the default, returns all characters.
`session` | (Optional) A Shiny session with a `numericInput` named `character_num` whose maximum should be updated.
`continuous` | Logical specifying whether characters are continuous. Treated as discrete if `FALSE`.
`tokens` | Vector of character strings corresponding to phylogenetic tokens.

### Value

`ExtractTaxa()` returns a matrix with n rows, each named for the relevant taxon, and c columns, each corresponding to the respective character specified in `character_num`.

`NexusTokens()` returns a character vector in which each entry corresponds to the states of a phylogenetic character, or a list containing an error message if input is invalid.

### Examples

    fileName <- paste0(system.file(package='TreeTools'),
                       '/extdata/input/dataset.nex')
    matrixLines <- readLines(fileName)[6:11]
    ExtractTaxa(matrixLines)

    NexusTokens('01[01]-?')

[Package TreeTools version 1.4.1 Index]