Convert between matrices and phyDat objects

MatrixToPhyDat() converts a matrix of tokens to a phyDat object; PhyDatToMatrix() converts a phyDat object to a matrix of tokens.

Usage

MatrixToPhyDat(tokens)

PhyDatToMatrix(
  dataset,
  ambigNA = FALSE,
  inappNA = ambigNA,
  parentheses = c("{", "}"),
  sep = ""
)

Arguments

tokens

Matrix of tokens, possibly created with ReadCharacters() or ReadTntCharacters(). Row names should correspond to leaf labels; column names may optionally correspond to character labels.

dataset

A dataset of class phyDat.

ambigNA, inappNA

Logical specifying whether to denote ambiguous / inapplicable characters as NA values.

parentheses

Character vector specifying style of parentheses with which to enclose ambiguous characters. c("[", "]") or "[]" will render [01]. NULL will use the token specified in the phyDat object; but beware that this will be treated as a distinct (non-ambiguous) token if re-encoding with PhyDatToMatrix().

sep

Character with which to separate ambiguous tokens, e.g. ',' will render [0,1].

Value

MatrixToPhyDat() returns an object of class phyDat.

PhyDatToMatrix() returns a matrix corresponding to the uncompressed character states within a phyDat object.

See also

Other phylogenetic matrix conversion functions: StringToPhyDat()

Author

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

Examples

tokens <- matrix(c(0, 0, "0", 0, 0,
                   0, 0, "1", 0, 1,
                   0, 0, "1", 0, 1,
                   0, 0, "2", 0, 1,
                   1, 1, "-", 1, 0,
                   1, 1, "2", 1, "{01}"),
                   nrow = 6, ncol = 5, byrow = TRUE,
                   dimnames = list(
                     paste0("Taxon_", LETTERS[1:6]),
                     paste0("Char_", 1:5)))
                   
MatrixToPhyDat(tokens)
#> $Taxon_A
#> [1] 1 1 1
#> 
#> $Taxon_B
#> [1] 1 2 2
#> 
#> $Taxon_C
#> [1] 1 2 2
#> 
#> $Taxon_D
#> [1] 1 3 2
#> 
#> $Taxon_E
#> [1] 2 4 1
#> 
#> $Taxon_F
#> [1] 2 3 5
#> 
#> attr(,"weight")
#> [1] 3 1 1
#> attr(,"nr")
#> [1] 3
#> attr(,"nc")
#> [1] 4
#> attr(,"index")
#> [1] 1 1 2 1 3
#> attr(,"levels")
#> [1] "-" "0" "1" "2"
#> attr(,"allLevels")
#> [1] "0"    "1"    "2"    "-"    "{01}"
#> attr(,"type")
#> [1] "USER"
#> attr(,"contrast")
#>      - 0 1 2
#> [1,] 0 1 0 0
#> [2,] 0 0 1 0
#> [3,] 0 0 0 1
#> [4,] 1 0 0 0
#> [5,] 0 1 1 0
#> attr(,"class")
#> [1] "phyDat"
data("Lobo", package = "TreeTools")
head(PhyDatToMatrix(Lobo.phy)[, 91:93])
#>                        [,1] [,2] [,3]
#> Tubiluchus_Priapulida  "-"  "0"  "0" 
#> Cricocosmia            "-"  "0"  "0" 
#> Aysheaia               "0"  "0"  "1" 
#> Siberion               "?"  "0"  "?" 
#> Onychodictyon_ferox    "0"  "0"  "1" 
#> Onychodictyon_gracilis "1"  "0"  "1"