Population and Evolutionary Genetics Analysis System


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Documentation for package ‘pegas’ version 0.3

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pegas-package Population and Evolutionary Genetics Analysis System
amova Analysis of Molecular Variance
as.loci Conversion Among Allelic Data Classes
as.loci.character Conversion Among Allelic Data Classes
as.loci.data.frame Conversion Among Allelic Data Classes
as.loci.factor Conversion Among Allelic Data Classes
as.loci.genind Conversion Among Allelic Data Classes
bind.loci Bind Loci Objects
cbind.loci Bind Loci Objects
edit.loci Edit Allelic Data with R's Data Editor
expand.genotype Utily Functions for pegas
Fst F-Statistics
genind2loci Conversion Among Allelic Data Classes
getAlleles Utily Functions for pegas
getGenotypes Utily Functions for pegas
getPloidy Utily Functions for pegas
H Heterozygosity at a Locus Using Gene Frequencies
haploNet Haplotype Networks
haplotype Haplotype Extraction and Frequencies
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
hw.test Test of Hardy-Weinberg Equilibrium
loci2genind Conversion Among Allelic Data Classes
MMD Mismatch Distribution
nuc.div Nucleotide Diversity
pegas Population and Evolutionary Genetics Analysis System
plot.haploNet Haplotype Networks
plot.haplotype Haplotype Extraction and Frequencies
plot.spectrum Site Frequency Spectrum
plot.summary.loci Print and Summaries of Loci Objects
print.amova Analysis of Molecular Variance
print.haplotype Haplotype Extraction and Frequencies
print.loci Print and Summaries of Loci Objects
print.summary.loci Print and Summaries of Loci Objects
R2.test Ramos-Onsins-Rozas Test of Neutrality
rbind.loci Bind Loci Objects
read.gtx Read Genetix Data Files
read.loci Read Allelic Data Files
site.spectrum Site Frequency Spectrum
summary.loci Print and Summaries of Loci Objects
tajima.test Test of the Neutral Mutation Hypothesis
theta.h Population Parameter THETA using Homozygosity
theta.k Population Parameter THETA using Expected Number of Alleles
theta.s Population Parameter THETA using Segregating Sites
theta.tree Population Parameter THETA Using Genealogy
write.loci Write Allelic Data Files
[.loci Print and Summaries of Loci Objects