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diveRsity (version 1.9.89)

A Comprehensive, General Purpose Population Genetics Analysis Package

Description

Allows the calculation of both genetic diversity partition statistics, genetic differentiation statistics, and locus informativeness for ancestry assignment. It also provides users with various option to calculate bootstrapped 95\% confidence intervals both across loci, for pairwise population comparisons, and to plot these results interactively. Parallel computing capabilities and pairwise results without bootstrapping are provided. Weir and Cockerham's 1984 F-statistics are also calculated. Various plotting features are also provided, as well as Chi-square tests of genetic heterogeneity are also provided. Functionality for the calculation of various diversity parameters is possible for RAD-seq derived SNP data sets containing thousands of marker loci. A shiny application for the development of microsatellite multiplexes is also available.

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Version

Install

install.packages('diveRsity')

Monthly Downloads

196

Version

1.9.89

License

GPL (>= 2)

Maintainer

Last Published

December 9th, 2016

Functions in diveRsity (1.9.89)

Pairwise directional differentiation heterozygosity components

Example input format for snp2gp function

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

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

Internal interactive plot generation

Efficient genepop reader

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

Rarefaction method for allelic richness

C++ level function for combining pw hsums

A function to calculate locus informative for the inference of ancestry

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

Bootstrapped allelic richness and heterozygosity

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

Calculates expected heterozygosity for divRatio

divMigrate bootstrap routine

Resample based calculation of allelic richness

Calculation of Weir and Cockerham's F-stats

C++ level observed heterozyosity calculation

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

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

C++ level observed heterozyosity calculation

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

C++ level allele frequency calculation

A faster function for calculating genetic differentiation statistics

Convert genos loci into presance absence matrices

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

C++ level observed heterozyosity calculation

Count alleles per locus

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

Similarity coefficients for co-dominant diploid genenotype data

divMigrateOnline

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

Randomly sample a genepop file

Genetic differentiation statistics and their estimators

Testing sample independence from genotype counts

Genepop and arlequin file conversion to data.frame

Memory efficient diversity statistic calculations

C++ level observed heterozyosity calculation

C++ level allele frequency calculation

Claculate basic descriptive population parameters from a genepop genotype file

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

Internal calculation of Rosenberg et al's In

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

Genetic differentiation statistics and their estimators

Pairwise diversity calculations for directional migration

pre.divLowMemory

Internal differentiation calculations

Internal differentiation calculator

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

C++ level observed heterozyosity calculation

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

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

Internal genepop file reader

A function to calculate allele frequencies from genepop files.

Generate bootstrap pairwise matrices per locus

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

regroup individuals in a genepop file according to an index

divMigrateOnline_test

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

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