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 interval |
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 |
crocrussula |
Genotypes and sex of 140 shrews Crocidura russula |
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 |
FST |
Wrapper for fst estimator from hierfstat package (from adegenet) |
fst |
Wrapper for fst estimator from hierfstat package (from adegenet) |
fstat |
Wrapper for fst estimator from hierfstat package (from adegenet) |
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 |
gstat.randtest |
Goudet's G-statistic Monte Carlo test for genind object |
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 |
pairwise.fst |
Wrapper for fst estimator from hierfstat package (from adegenet) |
pairwise.neifst |
Estimate pairwise FSTs according to Nei (1987) |
pairwise.WCfst |
Estimate pairwise FSTs according to Weir and Cockerham (1984) |
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 |
print.basic.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 |
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 |
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.t |
Simulate data from a non-equilibrium island model |
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.bayescan |
Writes a bayescan file |
write.fstat |
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 |