ExtractTaxa: Extract taxa from a matrix block

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Extract taxa from a matrix block

Description

Extract leaf labels and character states from a Nexus-formatted matrix.

Usage

ExtractTaxa(matrixLines, character_num = NULL, continuous = FALSE)

NexusTokens(tokens, character_num = NULL)

Arguments

matrixLines	Character vector containing lines of a file that include a phylogenetic matrix. See ReadCharacters() for expected format.
character_num	Index of character(s) to return. NULL, the default, returns all characters.
continuous	Logical specifying whether characters are continuous. Treated as discrete if FALSE.
tokens	Vector of character strings corresponding to phylogenetic tokens.

Value

ExtractTaxa() returns a matrix with n rows, each named for the relevant taxon, and c columns, each corresponding to the respective character specified in character_num.

NexusTokens() returns a character vector in which each entry corresponds to the states of a phylogenetic character, or a list containing an error message if input is invalid.

Examples

fileName <- paste0(system.file(package = "TreeTools"),
                   "/extdata/input/dataset.nex")
matrixLines <- readLines(fileName)[6:11]
ExtractTaxa(matrixLines)

NexusTokens("01[01]-?")

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.