dartR.base (version 1.0.5)

gl2paup.svdquartets: Converts a genlight object to nexus format PAUP SVDquartets

Description

The output nexus file contains the SNP data in one of two forms, depending upon what you regard as most appropriate. One form, that used by Chifman and Kubatko, has two lines per individual, one providing the reference SNP the second providing the alternate SNP (method=1). A second form, recommended by Dave Swofford, has a single line per individual, resolving heterozygous SNPs by replacing them with standard ambiguity codes (method=2). If the data are tag presence/absence, then method=2 is assumed.

Usage

gl2paup.svdquartets(
  x,
  outfile = "svd.nex",
  outpath = NULL,
  method = 2,
  nbootstraps = 10000,
  verbose = NULL
)

Value

returns no value (i.e. NULL)

Arguments

x

Name of the genlight object containing the SNP data or tag P/A data [required].

outfile

File name of the output file (including extension) [default 'svd.nex'].

outpath

Path where to save the output file [default global working directory or if not specified, tempdir()].

method

Method = 1, nexus file with two lines per individual; method = 2, nexus file with one line per individual, ambiguity codes for SNP genotypes, 0 or 1 for presence/absence data [default 2].

nbootstraps

Number of bootstrap replicates [default 10000]

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Author

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

References

Chifman, J. and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent. Bioinformatics 30: 3317-3324

See Also

Other linkers: gl2paup.parsimony()

Examples

gg <- testset.gl[1:20,1:100]
gg@other$loc.metrics <- gg@other$loc.metrics[1:100,]
gl2paup.svdquartets(gg, outpath=tempdir(),nbootstraps=100)