NexusTokensToInteger: Convert Nexus token matrix to integer

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Convert Nexus token matrix to integer

Description

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.

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.

Value

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

Author(s)

Martin R. Smith ([e-mail])

See Also

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

Examples

tokens <- matrix(c("0", "(12)", "1", "?", "-"),
                 nrow = 1,
                 dimnames = list("Taxon_A", paste0("C", 1:5)))
NexusTokensToInteger(tokens)
NexusTokensToInteger(tokens, polymorphism = "first")

TreeTools documentation built on June 2, 2026, 5:06 p.m.