TreeTools (version 1.4.1)

ReadCharacters: Read phylogenetic characters from file

Description

Parse a Nexus or TNT file, reading character states and names.

Usage

ReadCharacters(filepath, character_num = NULL, session = NULL)
ReadTntCharacters(filepath, character_num = NULL, type = NULL, session = NULL)
ReadAsPhyDat(filepath)
ReadTntAsPhyDat(filepath)
PhyDat(dataset)

Arguments

filepath

character string specifying location of file

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.

type

Character vector specifying categories of data to extract from file. Setting type = c('num', 'dna') will return only characters following a &[num] or &[dna] tag in a TNT input file. Leave as NULL (the default) to return all characters.

dataset

list of taxa and characters, in the format produced by read.nexus.data: a list of sequences each made of a single character vector, and named with the taxon name.

Value

ReadCharacters() and ReadTNTCharacters() return a matrix whose row names correspond to tip labels, and column names correspond to character labels, with the attribute state.labels listing the state labels for each character; or a list of length one containing a character string explaining why the function call was unsuccessful.

ReadAsPhyDat() and ReadTntAsPhyDat() return a phyDat object.

Functions

• PhyDat: A convenient wrapper for phangorn's phyDat(), which converts a list of morphological characters into a phyDat object. If your morphological characters are in the form of a matrix, perhaps because they have been read using read.table(), try MatrixToPhyDat() instead.

Details

Tested with matrices downloaded from MorphoBank, but should also work more widely; please report incorrectly parsed files.

Matrices must contain only continuous or only discrete characters; maximum one matrix per file. Continuous characters will be read as strings (i.e. base type 'character').

References

Maddison1997TreeTools

See Also

• Convert between matrices and phyDat objects: MatrixToPhyDat()

• Write characters to TNT-format file: WriteTntCharacters()

Examples

# NOT RUN {
fileName <- paste0(system.file(package='TreeTools'),
                   '/extdata/input/dataset.nex')
ReadCharacters(fileName)

fileName <- paste0(system.file(package='TreeTools'),
                   '/extdata/tests/continuous.nex')
continuous <- ReadCharacters(fileName)

# To convert from strings to numbers:
at <- attributes(continuous)
continuous <- suppressWarnings(as.numeric(continuous))
attributes(continuous) <- at
continuous
# }