read.nex: Read in NEXUS data

In celiason/phenotools: Tools for the analysis and assembly of phenomic data in R

Read in NEXUS data

Description

This function reads NEXUS data stored in nexus, text, or pdf files. Note: for pdf files, it is necessary to first install poppler with, e.g., 'brew install poppler'

Usage

read.nex(
  file,
  charlabels = NULL,
  charnums = NULL,
  statelabels = NULL,
  taxlabels = NULL,
  filename = NULL,
  ntax = NULL,
  nchar = NULL,
  first = NULL,
  last = NULL,
  missing = "?",
  gap = "-"
)

Arguments

file	(required) path to either a .nex, .txt, or .pdf file with NEXUS data
charlabels	optional path to text file with character statements
charnums	optional vector with character numbers
statelabels	optional character vector with state labels for characters
taxlabels	optional vector with names of taxa
filename	vector with names of files associated with characters
ntax	number of taxa (needed for PDF file reading)
nchar	number of characters (needed for PDF file reading)
first	first page for data matrix in a PDF file
last	last page for data matrix in a PDF file
missing	character representing missing data
gap	character representing inapplicable/incomporable data

Value

an object of class nex for use in further phenotools functions

Author(s)

Chad Eliason [e-mail]

References

Bertelli, S. and Chiappe, L. M. (2005). Earliest Tinamous (Aves: Palaeognathae) from the Miocene of Argentina and Their Phylogenetic Position. Contributions in Science, 502, 1-20.

Examples

## Not run: 
# Read in a nexus file:
x <- read.nex(file = system.file("extdata", "clarke_2006.nex",
package = "phenotools"))
# Build a `nex` object from text files:
charpath <- system.file("extdata", "brusatte2014_charlist.txt",
package = "phenotools")
matpath <- system.file("extdata", "brusatte2014_matrix.txt",
package = "phenotools")
x <- read.nex(matpath, charlabels=charpath)
# Build a `nex` object from a PDF file (Bertelli & Chiappe 2005):
x <- read.nex(file = system.file("extdata", "Bertelli_2005.pdf",
package = "phenotools"), ntax = 34, nchar = 63, first = 20, last = 22)
x
# Plot
plot(x, legend.pos = "top")

## End(Not run)

celiason/phenotools documentation built on Sept. 29, 2024, 5:43 p.m.