PhyToString: Convert between strings and 'phyDat' objects

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

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 ([e-mail])

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)

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.