R: Convert between strings and 'phyDat' objects

StringToPhyDat {TreeTools} | R Documentation

## Convert between strings and `phyDat` objects

### Description

`PhyDatToString()` converts a `phyDat` object as a string; `StringToPhyDat()` converts a string of character data to a `phyDat` object.

### Usage

    StringToPhyDat(string, tips, byTaxon = TRUE)

    StringToPhydat(string, tips, byTaxon = TRUE)

    PhyToString(
      phy,
      parentheses = "{",
      collapse = "",
      ps = "",
      useIndex = TRUE,
      byTaxon = TRUE,
      concatenate = TRUE
    )

    PhyDatToString(
      phy,
      parentheses = "{",
      collapse = "",
      ps = "",
      useIndex = TRUE,
      byTaxon = TRUE,
      concatenate = TRUE
    )

    PhydatToString(
      phy,
      parentheses = "{",
      collapse = "",
      ps = "",
      useIndex = TRUE,
      byTaxon = TRUE,
      concatenate = TRUE
    )

### Arguments

`string` | String of tokens, optionally containing whitespace, with no terminating semi-colon.
`tips` | (Optional) Character vector corresponding to the names (in order) of each taxon in the matrix, or an object such as a tree from which tip labels can be extracted.
`byTaxon` | Logical. If `TRUE`, write one taxon followed by the next. If `FALSE`, write one character followed by the next.
`phy` | An object of class `phyDat`.
`parentheses` | Character specifying format of parentheses with which to surround ambiguous tokens. Choose from: `{` (default), `[`, `(`, `<`.
`collapse` | Character specifying text, perhaps `,`, with which to separate multiple tokens within parentheses.
`ps` | Character specifying text, perhaps `;`, to append to the end of the string.
`useIndex` | Logical (default: `TRUE`) specifying whether to print duplicate characters multiple times, as they appeared in the original matrix.
`concatenate` | Logical specifying whether to concatenate all characters/taxa into a single string, or to return a separate string for each entry.

### Value

`StringToPhyDat()` returns an object of class `phyDat`.

`PhyToString()` returns a character vector listing a text representation of the phylogenetic character state for each taxon in turn.

### Author(s)

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

### See Also

Other phylogenetic matrix conversion functions: `MatrixToPhyDat()`

### Examples

    StringToPhyDat("-?01231230?-", c('Lion', 'Gazelle'), byTaxon = TRUE)
    # encodes the following matrix:
    # Lion     -?0123
    # Gazelle  1230?-

    fileName <- paste0(system.file(package='TreeTools'),
                       '/extdata/input/dataset.nex')
    phyDat <- ReadAsPhyDat(fileName)
    PhyToString(phyDat, concatenate = FALSE)

[Package TreeTools version 1.7.0 Index]