Bootstrap confidence intervals for variance components
Allelic frequencies
Read QuantiNemo extended format for genotype files
Example data set with 4 levels, one diploid and one haploid locus
Genotypes and sex of 140 shrews Crocidura russula
Writes a bayescan file
Converts genind objects from adegenet into a hierfstat data frame
Shuffles a sequence within groups defined by the input vector
individual counts
Simulate data from a non-equilibrium island model
Estimates variance components for each allele of a locus
Reads data from a FSTAT file
Tests the significance of the effect of test.lev on genetic differentiation
Test for sex biased dispersal
Calculates likelihood-ratio G-statistic on contingency table
Likelihood ratio G-statistic over loci
Estimate pairwise FSTs according to Nei (1987)
Estimate variance components and hierarchical F-statistics over all loci
Write ped file plink analysis
Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland
Calculates corrected Assignment Index
Goudet's G-statistic Monte Carlo test for genind object
Tests the significance of the effect of inner.level on genetic differentiation within blocks defined by outer.level
Estimate pairwise FSTs according to Weir and Cockerham (1984)
Example data set from Yang (1998) appendix
Estimate \(\beta\)s per population and a bootstrap confidence interval
General information on the hierfstat package
Shuffles a sequence
Converts diploid genotypic data into allelic data
Wrapper for fst estimator from hierfstat package (from adegenet)
Classical genetic distances estimation
Tests the significance of the effect of level on genetic differentiation
Shuffles a sequence among groups defined by the input vector
Tests the significance of the effect of test.lev on genetic differentiation
Separates diploid genotypes in its constituant alleles
Converts diploid genotypic data into allelic data
Performs bootstrapping over loci of pairwise Fst
Basic statistics
Allelic counts
Estimates allelic richness
Estimates euclidian distances
calculates euclidian distance among populations for a trait
Principal coordinate analysis
Performs bootstrapping over loci of population's Fis
Reads data from a FSTAT file
Number of different alleles
wrapper to return per locus variance components
Reads a vector into a matrix
Rewrite a matrix as a vecor
PCA on a matrix of individuals genotypes frequencies
Simulates frequencies, for internal use only
print function for pp.fst
Subsample a FSTAT data frame
Simulates genotypes in an island model at equilibrium
fst per pair
Computes Weir and Cockrham estimates of Fstatistics
Write an Fstat data file
Write structure file