| accessors | Accessors for adegenet objects |
| adegenet.package | The adegenet package |
| AICc | Compute Akaike Information Criterion for small samples (AICc)... |
| AIC.snapclust | Compute Akaike Information Criterion (AIC) for snapclust |
| ascore | Compute and optimize a-score for Discriminant Analysis of... |
| as.genlight | Conversion to class "genlight" |
| as-methods | Converting genind/genpop objects to other classes |
| as.SNPbin | Conversion to class "SNPbin" |
| auxil | Auxiliary functions for adegenet |
| BIC.snapclust | Compute Bayesian Information Criterion (BIC) for snapclust |
| chooseCN | Function to choose a connection network |
| colorplot | Represents a cloud of points with colors |
| compoplot | Genotype composition plot |
| coords.monmonier | Returns original points in results paths of an object of... |
| dapc | Discriminant Analysis of Principal Components (DAPC) |
| dapcGraphics | Graphics for Discriminant Analysis of Principal Components... |
| dapcIllus | Simulated data illustrating the DAPC |
| df2genind | Convert a data.frame of allele data to a genind object. |
| dist.genpop | Genetic distances between populations |
| doc_C_routines | Internal C routines |
| eHGDP | Extended HGDP-CEPH dataset |
| export_to_mvmapper | Export analysis for mvmapper visualisation |
| fasta2DNAbin | Read large DNA alignments into R |
| fasta2genlight | Extract Single Nucleotide Polymorphism (SNPs) from alignments |
| find.clusters | find.cluster: cluster identification using successive K-means |
| gengraph | Genetic transitive graphs |
| genind | adegenet formal class (S4) for individual genotypes |
| genind2df | Convert a genind object to a data.frame. |
| genind2genpop | Conversion from a genind to a genpop object |
| genlight | Formal class "genlight" |
| genpop | adegenet formal class (S4) for allele counts in populations |
| glAux | Auxiliary functions for genlight objects |
| glPca | Principal Component Analysis for genlight objects |
| glPlot | Plotting genlight objects |
| glSim | Simulation of simple genlight objects |
| H3N2 | Seasonal influenza (H3N2) HA segment data |
| haploGen | Simulation of genealogies of haplotypes |
| hierarchy-methods | Access and manipulate the population hierarchy for genind or... |
| Hs | Expected heterozygosity (Hs) |
| Hs.test | Test differences in expected heterozygosity (Hs) |
| HWE | Hardy-Weinberg Equilibrium test for multilocus data |
| hybridize | Function hybridize takes two genind in inputs and generates... |
| hybridtoy | Toy hybrid dataset |
| import2genind | Importing data from several softwares to a genind object |
| inbreeding | Likelihood-based estimation of inbreeding |
| isPoly | Assess polymorphism in genind/genpop objects |
| KIC | Compute Akaike Information Criterion for small samples (AICc)... |
| loadingplot | Represents a cloud of points with colors |
| makefreq | Compute allelic frequencies |
| microbov | Microsatellites genotypes of 15 cattle breeds |
| minorAllele | Compute minor allele frequency |
| monmonier | Boundary detection using Monmonier algorithm |
| mutations | Identify mutations between DNA sequences |
| nancycats | Microsatellites genotypes of 237 cats from 17 colonies of... |
| new.genind | genind constructor |
| new.genpop | genpop constructor |
| old2new | Convert objects with obsolete classes into new objects |
| pairDist | Pairwise distance plots |
| population-methods | Manipulate the population factor of genind objects. |
| propShared | Compute proportion of shared alleles |
| propTyped | Compute the proportion of typed elements |
| read.fstat | Reading data from Fstat |
| read.genepop | Reading data from Genepop |
| read.genetix | Reading data from GENETIX |
| read.PLINK | Reading PLINK Single Nucleotide Polymorphism data |
| read.snp | Reading Single Nucleotide Polymorphism data |
| read.structure | Reading data from STRUCTURE |
| repool | Pool several genotypes into a single dataset |
| rupica | Microsatellites genotypes of 335 chamois (Rupicapra... |
| scaleGen | Compute scaled allele frequencies |
| selpopsize | Select genotypes of well-represented populations |
| seploc | Separate data per locus |
| seppop | Separate genotypes per population |
| seqTrack | SeqTrack algorithm for reconstructing genealogies |
| sequences | Importing data from an alignement of sequences to a genind... |
| servers | Web servers for adegenet |
| showmekittens | When you need a break... |
| sim2pop | Simulated genotypes of two georeferenced populations |
| snapclust | Maximum-likelihood genetic clustering using EM algorithm |
| snapclust.choose.k | Choose the number of clusters for snapclust using AIC, BIC or... |
| SNPbin | Formal class "SNPbin" |
| snpposi | Analyse the position of polymorphic sites |
| snpzip | Identification of structural SNPs |
| spca | Spatial principal component analysis |
| spcaIllus | Simulated data illustrating the sPCA |
| spca_randtest | Monte Carlo test for sPCA |
| spca.rtests | Global and local tests |
| strata-methods | Access and manipulate the population strata for genind or... |
| swallowtails | Microsatellites genotypes of 781 swallowtail butterflies from... |
| tab | Access allele counts or frequencies |
| truenames | Restore true labels of an object |
| virClasses | Virtual classes for adegenet |
| web | Functions to access online resources for adegenet |
| xvalDapc | Cross-validation for Discriminant Analysis of Principal... |
