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

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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).

Author
Sebastien Rioux Paquette
Date of publication
2012-10-29 08:57:27
Maintainer
Sebastien Rioux Paquette <sebastien.riouxpaquette@gmail.com>
License
GPL-2
Version
1.0

View on CRAN

Man pages

batchconvert
Convert all Genepop files in dir to Arlequin format
batchconvertjack
Convert all Genepop files in dir to Arlequin format while...
batchjacklociArp
Remove a subset of loci from all Arlequin project files...
batchjacklociArpRANDOM
Remove a random subset of loci from all Arlequin project...
batchrecodeBi
Transform all multi-allelic Arlequin datafiles in dir to...
bootstrapHet
Calculate confidence intervals on observed and expected...
bootstrapHet_byloc
Calculate confidence intervals on observed and expected...
combineBsim
Combines real and simulated multilocus data (from the...
convert
Convert a Genepop file to Arlequin format
convertjack
Convert a Genepop file to Arlequin format while allowing the...
freqPCA
Create a table of allele frequencies from Arlequin file...
inputBottleSim
Create a BottleSim input file from a Genepop (.gen) file.
jacklociArp
Remove a subset of loci from a Arlequin project file...
jacklociArpRANDOM
Remove a random subset of loci from a Arlequin project file...
jackmsat
An internal function used by 'jackmsatpop'. Should not be...
jackmsatpop
From a Genepop input file (.gen), it calculates allele...
outputBottleSim
Converts alleles from BottleSim simulation results to real...
PICalc
Compute the polymorphism infomration content (PIC) of each...
popgen
Compute allele frequencies, population genetic parameters,...
PopGenKit-package
Useful functions for (batch) file conversion and data...
recodeBi
Transform a multi-allelic Arlequin datafile to a bi-allelic...

Files in this package

PopGenKit
PopGenKit/NAMESPACE
PopGenKit/extdata
PopGenKit/extdata/glyptemys3.arp
PopGenKit/extdata/glyptemys3.gen
PopGenKit/extdata/glyptemys2.gen
PopGenKit/extdata/glyptemys2.arp
PopGenKit/man
PopGenKit/man/batchrecodeBi.Rd
PopGenKit/man/bootstrapHet_byloc.Rd
PopGenKit/man/convert.Rd
PopGenKit/man/batchconvert.Rd
PopGenKit/man/recodeBi.Rd
PopGenKit/man/bootstrapHet.Rd
PopGenKit/man/jackmsat.Rd
PopGenKit/man/convertjack.Rd
PopGenKit/man/batchjacklociArp.Rd
PopGenKit/man/jacklociArpRANDOM.Rd
PopGenKit/man/PICalc.Rd
PopGenKit/man/combineBsim.Rd
PopGenKit/man/jackmsatpop.Rd
PopGenKit/man/PopGenKit-package.Rd
PopGenKit/man/outputBottleSim.Rd
PopGenKit/man/batchconvertjack.Rd
PopGenKit/man/freqPCA.Rd
PopGenKit/man/batchjacklociArpRANDOM.Rd
PopGenKit/man/inputBottleSim.Rd
PopGenKit/man/jacklociArp.Rd
PopGenKit/man/popgen.Rd
PopGenKit/DESCRIPTION
PopGenKit/MD5
PopGenKit/R
PopGenKit/R/jacklociArp.R
PopGenKit/R/batchjacklociArp.R
PopGenKit/R/jackmsatpop.R
PopGenKit/R/convert.R
PopGenKit/R/PICalc.R
PopGenKit/R/inputBottleSim.R
PopGenKit/R/batchconvertjack.R
PopGenKit/R/combineBsim.R
PopGenKit/R/batchjacklociArpRANDOM.R
PopGenKit/R/convertjack.R
PopGenKit/R/jackmsat.R
PopGenKit/R/bootstrapHet.R
PopGenKit/R/freqPCA.R
PopGenKit/R/popgen.R
PopGenKit/R/recodeBi.R
PopGenKit/R/outputBottleSim.R
PopGenKit/R/batchrecodeBi.R
PopGenKit/R/batchconvert.R
PopGenKit/R/jacklociArpRANDOM.R
PopGenKit/R/bootstrapHet_byloc.R
PopGenKit/R/PopGenKit-internal.R