| AIc |
Calculates corrected Assignment Index |
| allele.count |
Allelic counts |
| allelic.richness |
Estimates allelic richness |
| basic.stats |
Basic diversity and differentiation statistics |
| beta.dosage |
Estimates pairwise kinships and individual inbreeding coefficients from dosage data |
| betas |
Estimates betas per population and a bootstrap confidence interval |
| biall2dos |
Converts bi-allelic SNPs from hierfstat format to dosage format |
| boot.ppbetas |
Estimates bootstrap confidence intervals for pairwise betas FST estimates |
| boot.ppfis |
Performs bootstrapping over loci of population's Fis |
| boot.ppfst |
Performs bootstrapping over loci of pairwise Fst |
| boot.vc |
Bootstrap confidence intervals for variance components |
| cont.isl |
A genetic dataset from a diploid organism in a continent-island model |
| cont.isl99 |
A genetic dataset from a diploid organism in a continent-island model |
| crocrussula |
Genotypes and sex of 140 shrews Crocidura russula |
| diploid |
A genetic dataset from a diploid organism |
| exhier |
Example data set with 4 levels, one diploid and one haploid locus |
| fis.dosage |
Estimates F-statistics from dosage data |
| fs.dosage |
Estimates F-statistics from dosage data |
| fst.dosage |
Estimates F-statistics from dosage data |
| fstat2dos |
Converts a hierfstat genetic data frame to dosage data |
| g.stats |
Calculates likelihood-ratio G-statistic on contingency table |
| g.stats.glob |
Likelihood ratio G-statistic over loci |
| genet.dist |
Classical genetic distances estimation |
| genind2hierfstat |
Converts genind objects from adegenet into a hierfstat data frame |
| genot2al |
Separates diploid genotypes in its constituant alleles |
| getal |
Converts diploid genotypic data into allelic data |
| getal.b |
Converts diploid genotypic data into allelic data |
| grm2kinship |
Converts a Genetic Relationship Matrix (GRM) to a kinship matrix |
| gtrunchier |
Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland |
| hierfstat |
General information on the hierfstat package |
| Ho |
Basic diversity and differentiation statistics |
| Hs |
Basic diversity and differentiation statistics |
| ind.count |
individual counts |
| indpca |
PCA on a matrix of individuals genotypes frequencies |
| kinship2dist |
Converts a kinship matrix to a distance matrix |
| kinship2grm |
Converts a kinship matrix to a Genetic Relation Matrix (GRM) |
| kinshipShift |
Shifts a kinship matrix |
| mat2vec |
Creates a vector from a matrix |
| matching |
Estimates matching between pairs of individuals |
| ms2bed |
Import the output of the 'ms' program in a 'BED' object |
| ms2dos |
Import 'ms' output |
| nb.alleles |
Number of different alleles |
| pairwise.betas |
Estimates pairwise betas according to Weir and Goudet (2017) |
| pairwise.fst.dosage |
Estimates F-statistics from dosage data |
| pairwise.neifst |
Estimates pairwise FSTs according to Nei (1987) |
| pairwise.WCfst |
Estimates pairwise FSTs according to Weir and Cockerham (1984) |
| pcoa |
Principal coordinate analysis |
| pi.dosage |
Estimates nucleotide diversity (pi) from dosage data |
| plot.fs.dosage |
Estimates F-statistics from dosage data |
| plot.indpca |
PCA on a matrix of individuals genotypes frequencies |
| pop.freq |
Allelic frequencies |
| pp.fst |
fst per pair |
| pp.sigma.loc |
wrapper to return per locus variance components |
| print.basic.stats |
Basic diversity and differentiation statistics |
| print.betas |
Estimates betas per population and a bootstrap confidence interval |
| print.boot.ppfst |
Performs bootstrapping over loci of pairwise Fst |
| print.fs.dosage |
Estimates F-statistics from dosage data |
| print.indpca |
PCA on a matrix of individuals genotypes frequencies |
| print.pp.fst |
print function for pp.fst |
| print.wc |
Computes Weir and Cockrham estimates of Fstatistics |
| qn2.read.fstat |
Read QuantiNemo extended format for genotype files Read QuantiNemo (<http://www2.unil.ch/popgen/softwares/quantinemo/>) genotype files extended format (option 2) |
| read.fstat |
Reads data from a FSTAT file |
| read.fstat.data |
Reads data from a FSTAT file |
| read.ms |
Read data generated by Hudson ms program Read data generated by Hudson ms program, either as Haplotypes or as SNPs. |
| read.VCF |
Reads a VCF file into a BED object |
| samp.between |
Shuffles a sequence among groups defined by the input vector |
| samp.between.within |
Shuffles a sequence |
| samp.within |
Shuffles a sequence within groups defined by the input vector |
| sexbias.test |
Test for sex biased dispersal |
| sim.freq |
Simulates frequencies, for internal use only |
| sim.genot |
Simulates genotypes in an island model at equilibrium |
| sim.genot.metapop.t |
Simulate genetic data from a metapopulation model |
| sim.genot.t |
Simulate data from a non equilibrium continent-island model |
| subsampind |
Subsample a FSTAT data frame |
| TajimaD.dosage |
Estimates Tajima's D |
| test.between |
Tests the significance of the effect of test.lev on genetic differentiation |
| test.between.within |
Tests the significance of the effect of test.lev on genetic differentiation |
| test.g |
Tests the significance of the effect of level on genetic differentiation |
| test.within |
Tests the significance of the effect of inner.level on genetic differentiation within blocks defined by outer.level |
| theta.Watt.dosage |
Estimates theta_{Watterson} from dosage data |
| varcomp |
Estimates variance components for each allele of a locus |
| varcomp.glob |
Estimate variance components and hierarchical F-statistics over all loci |
| vec2mat |
Fills a triangular matrix from the inputed vector |
| wc |
Computes Weir and Cockrham estimates of Fstatistics |
| write.bayescan |
Writes a bayescan file |
| write.fstat |
Write an Fstat data file |
| write.ped |
Write ped file for analyses with PLINK |
| write.struct |
Write structure file |
| yangex |
Example data set from Yang (1998) appendix |
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