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)
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> ____1 "'" "C" "h" "a" "r" "a" "c" "t" "e" "r" "o" "n" "e"
#> ____2 "C" "h" "a" "r" "a" "c" "t" "e" "r" "_" "t" "w" "o"
#> ____3 "'" "l" "o" "t" "s" "-" "o" "f" "-" "p" "u" "n" "c"
#> ____4 "C" "h" "a" "r" "a" "c" "t" "e" "r" "_" "n" "/" "a"
#> ____5 "C" "h" "a" "r" "a" "c" "t" "e" "r" "_" "5" "/" "s"
#> ____6 "C" "h" "a" "r" "a" "c" "t" "e" "r" "_" "6" "/" NA
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
#> ____1 "'" "/" "a" "b" "s" "e" "n" "t" "p" "r" "e" "s"
#> ____2 "/" "a" "b" "s" "e" "n" "t" "p" "r" "e" "s" "e"
#> ____3 "t" "u" "a" "t" "i" "o" "n" "," "a" "n" "d" "\""
#> ____4 "_" "l" "o" "n" "g" "_" "d" "e" "s" "c" "r" "i"
#> ____5 "i" "m" "p" "l" "e" "m" "o" "r" "e" "_" "c" "o"
#> ____6 NA NA NA NA NA NA NA NA NA NA NA NA
#> [,26] [,27] [,28] [,29]
#> ____1 "e" "n" "t" ","
#> ____2 "n" "t" "," NA
#> ____3 "s" "o" "o" "n"
#> ____4 "p" "t" "i" "o"
#> ____5 "m" "p" "l" "e"
#> ____6 NA NA NA NA
NexusTokens("01[01]-?")
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] "0" "1" "[01]" "-" "?"