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Convert between strings and phyDat objects

Source: R/parse_files.R
PhyToString.Rd

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.

See also

Other phylogenetic matrix conversion functions: MatrixToPhyDat()

Author

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

Examples

StringToPhyDat("-?01231230?-", c("Lion", "Gazelle"), byTaxon = TRUE)
#> $Lion
#> [1] 1 3 5 2 4 6
#> 
#> $Gazelle
#> [1] 2 4 6 5 3 1
#> 
#> attr(,"weight")
#> [1] 1 1 1 1 1 1
#> attr(,"nr")
#> [1] 6
#> attr(,"nc")
#> [1] 5
#> attr(,"index")
#> [1] 1 2 3 4 5 6
#> attr(,"levels")
#> [1] "-" "0" "1" "2" "3"
#> attr(,"levels")attr(,".match.hash")
#> <hash table>
#> attr(,"allLevels")
#> [1] "-" "1" "?" "2" "0" "3"
#> attr(,"type")
#> [1] "USER"
#> attr(,"contrast")
#>      - 0 1 2 3
#> [1,] 1 0 0 0 0
#> [2,] 0 0 1 0 0
#> [3,] 1 1 1 1 1
#> [4,] 0 0 0 1 0
#> [5,] 0 1 0 0 0
#> [6,] 0 0 0 0 1
#> attr(,"class")
#> [1] "phyDat"
# 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)
#> [1] "0000000" "0000000" "1111?00" "111??11" "1111?11"