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PopGenKit (version 1.0)

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

Description

There are two main purposes to this package. The first is to allow batch conversion of Genepop (Rousset 2008) input files for use with Arlequin (Excoffier and Lischer 2010), which has a simple GUI to analyze batch files. Two commonly used simulation software, BottleSim (Kuo & Janzen 2003) and Easypop (Balloux 2001) produce Genepop output files that can be analyzed this way. There are also functions to convert to and from BottleSim format, to quickly produce allele frequency tables or to convert a file directly for use in ordination analyses (e.g. principal component analysis). This package also includes functions to calculate allele rarefaction curves, confidence intervals on heterozygosity and allelic richness with resampling strategies (bootstrap and jackknife).

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Version

Install

install.packages('PopGenKit')

Monthly Downloads

6

Version

1.0

License

GPL-2

Maintainer

Sebastien Rioux Paquette

Last Published

October 29th, 2012

Functions in PopGenKit (1.0)

batchconvertjack

Convert all Genepop files in dir to Arlequin format while removing any subset of loci

Create a table of allele frequencies from Arlequin file (.arp) that can be used directly for ordination analyses (e.g. Principal Component Analysis)

Convert a Genepop file to Arlequin format

Combines real and simulated multilocus data (from the software BottleSim) in new Genepop files (one file per simulation replicate).

batchjacklociArpRANDOM

Remove a random subset of loci from all Arlequin project files (extension .arp) in dir

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

Calculate confidence intervals on observed and expected heterozygosity by bootstrapping individuals in each population

bootstrapHet_byloc

Calculate confidence intervals on observed and expected heterozygosity in each population by bootstrapping markers

Transform a multi-allelic Arlequin datafile to a bi-allelic datafile

Compute allele frequencies, population genetic parameters, and pairwise Fst values from a Arlequin (.arp) input file

jacklociArpRANDOM

Remove a random subset of loci from a Arlequin project file (extension .arp)

An internal function used by jackmsatpop. Should not be used.

Transform all multi-allelic Arlequin datafiles in dir to bi-allelic datafiles

Compute the polymorphism infomration content (PIC) of each locus in a Arlequin project file (.arp)

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

From a Genepop input file (.gen), it calculates allele rarefaction curves within each population for a given sampling interval.

outputBottleSim

Converts alleles from BottleSim simulation results to real allele sizes as found in the input file generated with the function inputBottleSim

batchjacklociArp

Remove a subset of loci from all Arlequin project files (extension .arp) in dir

PopGenKit-package

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

Remove a subset of loci from a Arlequin project file (extension .arp)

Convert all Genepop files in dir to Arlequin format