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

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).

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

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...

Functions

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.