A Comprehensive, General Purpose Population Genetics Analysis Package

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Documentation for package ‘diveRsity’ version 1.9.90

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arp2gen Fast and simple conversion of arlequin (.arp) genotype files to genepop files, form within the 'R' environment.
basicStats Claculate basic descriptive population parameters from a genepop genotype file
bigDivPart Genetic differentiation statistics and their estimators for high throughput data (e.g. RAD-seq derived SNPS)
Big_data Example infile for diveRsity package
chiCalc Testing sample independence from genotype counts
corPlot A function to plot the relationship between Gst, G'st, Theta, D (Jost) and the mean number of alleles at a locus. A reimplementation of 'corPlot'. This function will replace the old function in later version of the package.
diffCalc A faster function for calculating genetic differentiation statistics
diffPlot A function to plot pairwise statistics calculated by divPart.
divBasic A function to calculate basic population parameters such as allelic richness, observed heterozygosity, as well as expected heterozygosity.
divMigrate An experimental function for the detection of directional differentiation from microsatellite data.
divOnline A function to launch a web app version of 'diveRsity' from the local system.
divPart Genetic differentiation statistics and their estimators
divRatio Calculates the standardised diversity ratios relative to a 'yardstick' reference population following Skrbinsek et al., 2012.
divSimCo Similarity coefficients for co-dominant diploid genenotype data
fastDivPart Genetic differentiation statistics and their estimators
fstOnly A minimal function for the calculate of Weir & Cockerham's (1984) F_ST and F_IT from codominant molecular data in the genepop format.
gpSampler Randomly sample a genepop file
haploDiv A function, allowing the calculation of Weir & Cockerham's (1984) F_{ST} from haploid genotypes in the genepop
inCalc A function to calculate locus informative for the inference of ancestry
microPlexer Launches a 'shiny' app for the arrangement of microsatellite loci into size and fluorophore based multiplex groups.
polyIn A function for calculating informativeness for the inference of ancestry from loci of any ploidy.
pop_stats Example pop_stats data frame for use in the function 'divRatio'
readGenepop A function to calculate allele frequencies from genepop files.
snp2gen Conversion function for SNP nucleotide genotype matrix to a genepop file.
SNPs Example input format for 'snp2gp' function
Test_data Example infile for diveRsity package