write.nex: Write a nexus data object to a file

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

Write a nexus data object to a file

Description

Function to write nexus file to data for, e.g., analysis in MESQUITE, etc.

Usage

write.nex(
  x,
  file,
  missing = NULL,
  gap = NULL,
  mrbayes = FALSE,
  ngen = NULL,
  phy = NULL,
  run = FALSE,
  format = c("nexus", "tnt")
)

Arguments

x	(required) nexus file ('nex') object
file	file patch for exported file
missing	character representing missing data
gap	character representing incomparable data
mrbayes	whether to add mrbayes block to output
ngen	number of generations to run in mrbyaes
phy	input phylogeny for downstream analysis in mrbayes
run	whether to run TNT analysis
format	output formate

Value

an object of class nex for use in further phenotools functions

Author(s)

Chad Eliason [e-mail]

Examples

## Not run: 
x <- read.nex(file = system.file("extdata", "clarke_2006.nex",
package = "phenotools"))
write.nex(x, file='test.nex')

## End(Not run)

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