convertjack: Convert a Genepop file to Arlequin format while allowing the removal of any subset of loci from the output

Description

This function converts a datafile from Genepop format (extension .gen) to Arlequin project file format (extension .arp). The user can specify which loci to remove so that only the others will be included in the output file.

Usage

convertjack(datafile, ndigit = 3, rm.loci)

Arguments

datafile

Name of the file to convert, with the extension (e.g. 'glyptemys3.gen').

ndigit

The number of digits per allele in the input file. Can be 2 or 3 (default is 3).

rm.loci

A vector indicating which locus or loci to remove from the final output file. Loci should be indicated as numbers according to the order in which they are listed in the input file (e.g. c(1,3) would remove the first and third loci).

Value

A file with the same file name as the input file, but with the .arp extension (Arlequin) will be saved in the working directory.

Details

Input file must end with the extension '.gen'. Make sure to follow standard Genepop format for input file. The IDs of all individuals should be immediately followed by a comma. Population labels should be Pop, POP, or pop. There should not be invisible characters (tabs or spaces) at the end of lines, especially lines on which population labels are found. These lines should have only three characters (Pop). See example file 'glyptemys3.gen' if needed. For converting multiple files, use the function batchconvertjack instead.

References