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

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Documentation for package ‘PopGenKit’ version 1.0

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PopGenKit-package Useful functions for (batch) file conversion and data resampling in microsatellite datasets
batchconvert Convert all Genepop files in dir to Arlequin format
batchconvertjack Convert all Genepop files in dir to Arlequin format while removing any subset of loci
batchjacklociArp Remove a subset of loci from all Arlequin project files (extension .arp) in dir
batchjacklociArpRANDOM Remove a random subset of loci from all Arlequin project files (extension .arp) in dir
batchrecodeBi Transform all multi-allelic Arlequin datafiles in dir to bi-allelic datafiles
bootstrapHet 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
combineBsim Combines real and simulated multilocus data (from the software BottleSim) in new Genepop files (one file per simulation replicate).
convert Convert a Genepop file to Arlequin format
convertjack Convert a Genepop file to Arlequin format while allowing the removal of any subset of loci from the output
freqPCA Create a table of allele frequencies from Arlequin file (.arp) that can be used directly for ordination analyses (e.g. Principal Component Analysis)
inputBottleSim Create a BottleSim input file from a Genepop (.gen) file.
jacklociArp Remove a subset of loci from a Arlequin project file (extension .arp)
jacklociArpRANDOM Remove a random subset of loci from a Arlequin project file (extension .arp)
jackmsat An internal function used by 'jackmsatpop'. Should not be used.
jackmsatpop 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'
PICalc Compute the polymorphism infomration content (PIC) of each locus in a Arlequin project file (.arp)
popgen Compute allele frequencies, population genetic parameters, and pairwise Fst values from a Arlequin (.arp) input file
PopGenKit Useful functions for (batch) file conversion and data resampling in microsatellite datasets
recodeBi Transform a multi-allelic Arlequin datafile to a bi-allelic datafile