Estimation and Tests of Hierarchical F-Statistics

AIc | Calculates corrected Assignment Index |

allele.count | Allelic counts |

allelic.richness | Estimates allelic richness |

basic.stats | Basic statistics |

betas | Estimate betas per population and a bootstrap confidence... |

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... |

cont.isl99 | A genetic dataset from a diploid organism in a... |

crocrussula | Genotypes and sex of 140 shrews Crocidura russula |

diploid | A genetic dataset from a diploid organism |

eucl.dist | Estimates euclidian distances |

eucl.dist.trait | calculates euclidian distance among populations for a trait |

exhier | Example data set with 4 levels, one diploid and one haploid... |

fstat.from.adegenet | Wrapper for fst estimator from hierfstat package (from... |

genet.dist | Classical genetic distances estimation |

genind2hierfstat | Converts genind objects from adegenet into a hierfstat data... |

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 |

gstat.randtest | Goudet's G-statistic Monte Carlo test for genind object |

g.stats | Calculates likelihood-ratio G-statistic on contingency table |

g.stats.glob | Likelihood ratio G-statistic over loci |

gtrunchier | Genotypes at 6 microsatellite loci of Galba truncatula from... |

hierfstat | General information on the hierfstat package |

ind.count | individual counts |

indpca | PCA on a matrix of individuals genotypes frequencies |

mat2vec | Rewrite a matrix as a vecor |

nb.alleles | Number of different alleles |

pairwise.neifst | Estimate pairwise FSTs according to Nei (1987) |

pairwise.WCfst | Estimate pairwise FSTs according to Weir and Cockerham (1984) |

pcoa | Principal coordinate analysis |

pop.freq | Allelic frequencies |

ppfst | fst per pair |

pp.sigma.loc | wrapper to return per locus variance components |

print.pp.fst | print function for pp.fst |

qn2.read.fstat | Read QuantiNemo extended format for genotype files |

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.ms.snps | Read data generated by Hudson ms program |

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 |

test.between | Tests the significance of the effect of test.lev on genetic... |

test.between.within | Tests the significance of the effect of test.lev on genetic... |

test.g | Tests the significance of the effect of level on genetic... |

test.within | Tests the significance of the effect of inner.level on... |

varcomp | Estimates variance components for each allele of a locus |

varcomp.glob | Estimate variance components and hierarchical F-statistics... |

vec2mat | Reads a vector into a matrix |

wc | Computes Weir and Cockrham estimates of Fstatistics |

write.bayescan | Writes a bayescan file |

writefstat | Write an Fstat data file |

write.ped | Write ped file plink analysis |

write.struct | Write structure file |

yangex | Example data set from Yang (1998) appendix |

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