inputBottleSim: Create a BottleSim input file from a Genepop (.gen) file.

Description

This function creates a genotype input file for use with the population genetics simulation software BottleSim (Kuo and Janzen 2003). It also saves all required allele information to allow retro-conversion of BottleSim simulation results back to original alleles with the function outputBottleSim.

Usage

inputBottleSim(datafile, ndigit = 3)

Arguments

datafile

Name of the input Genepop file with the extension (e.g. 'glyptemys3.gen')

ndigit

Number of digits per allele in input file. Can be 2 or 3 (default 3).

Value

The BottleSim file and the 'alleles' file will be saved in the working directory

Details

Two files will be created after using this function; one is the BottleSim input file, the other is called 'alleles'. This file is required to retro-convert BottleSim results back to the original format with outputBottleSim. Do not modify or erase this file. 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.

References