rad2nex: Export a 'rad.mat' object to a Nexus file

In andrew-hipp/RADami: Phylogenetic Analysis of RADseq Data

Export a rad.mat object to a Nexus file

Description

This function takes output from rad2mat and writes it to a Nexus file, ready for analysis by PAUP*, BEAST, or other software

Usage

rad2nex(pyDat, inds = row.names(pyDat), indNames = NA,
        fillBlanks = NA, fillChar = '-',
        loci = dimnames(pyDat)[[2]],
        outfile = 'pyMat.out.nex',
        verbose = FALSE,
        logfile = 'rad2nex.log', ...)

Arguments

pyDat	an object of class rad.mat
inds	individuals to include in the export
indNames	a vector of names to rename individuals if desired; assumed to be in same order as inds
fillBlanks	integer; number of characters to fill blanks with
fillChar	character to fill blanks with
loci	loci to include in the Nexus file, by name
outfile	file name to write
verbose	boolean; report number of characters to add to file
logfile	name of logfile, which holds the names of loci in the phylip file written

Value

No value. This function is called for the side-effect of writing a Nexus file

Author(s)

Andrew Hipp

See Also

rad2mat, rad2phy, write.DNAStringSet

andrew-hipp/RADami documentation built on Nov. 9, 2023, 5:40 p.m.