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

In PopGenKit: Useful functions for (batch) file conversion and data resampling in microsatellite datasets

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).

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.

Value

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

Author(s)

Sebastien Rioux Paquette

References

Kuo C.H., and F.J.Janzen (2003). BottleSim: a bottleneck simulation program for long-lived species with overlapping generations. Mol. Ecol. Notes, 3, 669-673.

Rousset, F. (2008). Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Res. 8: 103-106.

See Also

outputBottleSim, combineBsim

PopGenKit documentation built on May 2, 2019, 3:33 p.m.