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]