TreeTools: PhyToString – R documentation

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PhyToString

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`	Character vector corresponding to the names (in order) of each taxon in the matrix.
`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)

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)

TreeTools

Create, Modify and Analyse Phylogenetic Trees

v1.4.4

GPL (>= 3)

Authors

Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)

Initial release