# A Comprehensive, General Purpose Population Genetics Analysis Package

## Documentation for package ‘diveRsity’ version 1.9.90

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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