diveRsity

Count alleles per locus

Example infile for diveRsity package

Calculates expected heterozygosity for divRatio

Example input format for snp2gp function

C++ level allele frequency calculation

Example infile for diveRsity package

C++ level observed heterozyosity calculation

Bootstrapped allelic richness and heterozygosity

Resample based calculation of allelic richness

Fast and simple conversion of arlequin (.arp) genotype files to genepop files, form within the R environment.

Claculate basic descriptive population parameters from a genepop genotype file

Genetic differentiation statistics and their estimators for high throughput data (e.g. RAD-seq derived SNPS)

Memory efficient diversity statistic calculations

divMigrate bootstrap routine

C++ level observed heterozyosity calculation

Testing sample independence from genotype counts

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.

An internal function for plotting the relationship between differentiation and locus polymorphism

A faster function for calculating genetic differentiation statistics

C++ level function for global total and sub-population heterozygosity

A function to plot pairwise statistics calculated by divPart.

A function to calculate basic population parameters such as allelic richness, observed heterozygosity, as well as expected heterozygosity.

An experimental function for the detection of directional differentiation from microsatellite data.

An experimental function for the detection of directional differentiation from microsatellite data.

An experimental function for the detection of directional differentiation from microsatellite data.

A function to launch a web app version of diveRsity from the local system.

Genetic differentiation statistics and their estimators

Calculates the standardised diversity ratios relative to a 'yardstick' reference population following Skrbinsek et al., 2012.

Similarity coefficients for co-dominant diploid genenotype data

C++ level observed heterozyosity calculation

Genetic differentiation statistics and their estimators

Genepop and arlequin file conversion to data.frame

A minimal function for the calculate of Weir & Cockerham's (1984) F_ST and F_IT from codominant molecular data in the genepop format.

Calculation of Weir and Cockerham's F-stats

Convert genos loci into presance absence matrices

C++ level function for Weir & Cockerham F-stats

Randomly sample a genepop file

A function, allowing the calculation of Weir & Cockerham's (1984) F_{ST} from haploid genotypes in the genepop

C++ level function for global total and sub-population heterozygosity

C++ level observed heterozyosity calculation

A function to calculate locus informative for the inference of ancestry

Internal calculation of Rosenberg et al's In

Launches a shiny app for the arrangement of microsatellite loci into size and fluorophore based multiplex groups.

Winston Chang's multiplot function for arranging ggplots into a grid

C++ level allele frequency calculation

C++ level observed heterozyosity calculation

Internal interactive plot generation

A function for calculating informativeness for the inference of ancestry from loci of any ploidy.

Example pop_stats data frame for use in the function divRatio

Internal differentiation calculations

Pairwise diversity calculations for directional migration

C++ level calculation of total and sub-population heterozygosity

Pairwise directional differentiation heterozygosity components

C++ level function for generating pairwise hsums for fst calculation

C++ level function for pairwise Weir & Cockerham F-stats

Rarefaction method for allelic richness

A function to calculate allele frequencies from genepop files.

Internal genepop file reader

regroup individuals in a genepop file according to an index

Efficient genepop reader

Conversion function for SNP nucleotide genotype matrix to a genepop file.

Internal differentiation calculator

C++ level function for combining pw hsums

C++ level function for global total and sub-population heterozygosity

Generate bootstrap pairwise matrices per locus