Convert Nexus token matrix to integer

NexusTokensToInteger() converts the character matrix returned by ReadCharacters() to an integer matrix, mapping polymorphic, ambiguous (?), and inapplicable (-) tokens to NA_integer_ or to the first/last state listed in the polymorphism, depending on polymorphism.

Usage

NexusTokensToInteger(tokens, polymorphism = c("?", "first", "last"))

Arguments

tokens

Character matrix as returned by ReadCharacters(), a character vector as returned by NexusTokens(), or a phyDat object.

polymorphism

Character string specifying how to handle polymorphic tokens such as "(01)" or "{12}":

"?" (default)

Treat as the NEXUS missing-data token: map to NA_integer_.

"first"

Use the first state digit inside the brackets.

"last"

Use the last state digit inside the brackets.

Tokens "?" and "-" always map to NA_integer_ regardless of polymorphism.

Value

An integer matrix (or vector) with the same dimensions and dimnames as tokens.

Details

Only digit states 0..9 are recognised; non-digit symbols (and any token whose interior contains no digits) become NA_integer_. Polymorphism extraction (polymorphism = "first"/"last") likewise considers digits only.

If tokens is a phyDat object it is first converted via PhyDatToMatrix() with ambigNA = TRUE, inappNA = TRUE, so that fully-ambiguous and inapplicable rows become NA_integer_ and only true partial polymorphisms are subject to the polymorphism rule.

See also

Other phylogenetic matrix conversion functions: Decompose(), MatrixToPhyDat(), Reweight(), StringToPhyDat()

Author

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

Examples

tokens <- matrix(c("0", "(12)", "1", "?", "-"),
                 nrow = 1,
                 dimnames = list("Taxon_A", paste0("C", 1:5)))
NexusTokensToInteger(tokens)
#>         C1 C2 C3 C4 C5
#> Taxon_A  0 NA  1 NA NA
NexusTokensToInteger(tokens, polymorphism = "first")
#>         C1 C2 C3 C4 C5
#> Taxon_A  0  1  1 NA NA