PopGenKit: Useful functions for (batch) file conversion and data resampling in microsatellite datasets
Version 1.0

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).

Browse man pages Browse package API and functions Browse package files

AuthorSebastien Rioux Paquette
Date of publication2012-10-29 08:57:27
MaintainerSebastien Rioux Paquette <sebastien.riouxpaquette@gmail.com>
LicenseGPL-2
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PopGenKit")

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...

Functions

PICalc Man page Source code
PopGenKit Man page
PopGenKit-package Man page
batchconvert Man page Source code
batchconvertjack Man page Source code
batchjacklociArp Man page Source code
batchjacklociArpRANDOM Man page Source code
batchrecodeBi Man page Source code
bootstrapHet Man page Source code
bootstrapHet_byloc Man page Source code
combineBsim Man page Source code
convert Man page Source code
convertjack Man page Source code
freqPCA Man page Source code
inputBottleSim Man page Source code
jacklociArp Man page Source code
jacklociArpRANDOM Man page Source code
jackmsat Man page Source code
jackmsatpop Man page Source code
outputBottleSim Man page Source code
popgen Man page Source code
recodeBi Man page Source code

Files

NAMESPACE
extdata
extdata/glyptemys3.arp
extdata/glyptemys3.gen
extdata/glyptemys2.gen
extdata/glyptemys2.arp
man
man/batchrecodeBi.Rd
man/bootstrapHet_byloc.Rd
man/convert.Rd
man/batchconvert.Rd
man/recodeBi.Rd
man/bootstrapHet.Rd
man/jackmsat.Rd
man/convertjack.Rd
man/batchjacklociArp.Rd
man/jacklociArpRANDOM.Rd
man/PICalc.Rd
man/combineBsim.Rd
man/jackmsatpop.Rd
man/PopGenKit-package.Rd
man/outputBottleSim.Rd
man/batchconvertjack.Rd
man/freqPCA.Rd
man/batchjacklociArpRANDOM.Rd
man/inputBottleSim.Rd
man/jacklociArp.Rd
man/popgen.Rd
DESCRIPTION
MD5
R
R/jacklociArp.R
R/batchjacklociArp.R
R/jackmsatpop.R
R/convert.R
R/PICalc.R
R/inputBottleSim.R
R/batchconvertjack.R
R/combineBsim.R
R/batchjacklociArpRANDOM.R
R/convertjack.R
R/jackmsat.R
R/bootstrapHet.R
R/freqPCA.R
R/popgen.R
R/recodeBi.R
R/outputBottleSim.R
R/batchrecodeBi.R
R/batchconvert.R
R/jacklociArpRANDOM.R
R/bootstrapHet_byloc.R
R/PopGenKit-internal.R
PopGenKit documentation built on May 20, 2017, 4:43 a.m.