R: Convert between matrices and 'phyDat' objects

MatrixToPhyDat {TreeTools} | R Documentation

## Convert between matrices and `phyDat` objects

### Description

`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)

### 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.

### Value

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

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

### Author(s)

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

### See Also

Other phylogenetic matrix conversion functions: `StringToPhyDat()`

### 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)

[Package TreeTools version 1.7.2 Index]