TreeTools (version 1.4.1)

ExtractTaxa: Extract taxa from a matrix block

Description

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

Usage

ExtractTaxa(
  matrixLines,
  character_num = NULL,
  session = NULL,
  continuous = FALSE
)
NexusTokens(tokens, character_num = NULL, session = 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.

session

(Optional) A Shiny session with a numericInput named character_num whose maximum should be updated.

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

# NOT RUN {
fileName <- paste0(system.file(package='TreeTools'),
                   '/extdata/input/dataset.nex')
matrixLines <- readLines(fileName)[6:11]
ExtractTaxa(matrixLines)

NexusTokens('01[01]-?')
# }