allele.count |
Allelic counts |
allelic.richness |
Estimates allelic richness |
basic.stats |
Basic statistics |
betai |
Estimation of beta per population |
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 |
cfe.dist |
Estimates Cavalli-Sforza & Edwards Chord distance |
da.dist |
Estimates Nei's DA distance |
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 locus |
g.stats |
Calculates likelihood-ratio G-statistic on contingency table |
g.stats.glob |
Likelihood ratio G-statistic over loci |
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 |
gtrunchier |
Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland |
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 |
nei.dist |
Estimates Nei's genetic distance |
pcoa |
Principal coordinate analysis |
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 |
prepdata |
Sort and renumber and recode levels for the hierarchical analysis if necessary |
print.bas.stats |
Basic statistics |
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 |
read.fstat |
Reads data from a FSTAT file |
read.fstat.data |
Reads data from a FSTAT file |
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 |
sim.freq |
Simulates frequencies, for internal use only |
sim.genot |
Simulates genotypes in an island model at equilibrium |
subsampind |
Subsample a FSTAT data frame |
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 |
varcomp |
Estimates variance components for each allele of a locus |
varcomp.glob |
Estimate variance components and hierarchical F-statistics over all loci |
vec2mat |
Reads a vector into a matrix |
wc |
Computes Weir and Cockrham estimates of Fstatistics |
write.fstat |
Write an Fstat data file |
write.struct |
Write structure file |
yangex |
Example data set from Yang (1998) appendix |