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| adegenet-package | The adegenet package |
| $,genind-method | adegenet formal class (S4) for individual genotypes |
| $,genpop-method | adegenet formal class (S4) for allele counts in populations |
| $,pdata-method | Accessors for adegenet objects |
| $,phylo4-method | Accessors for adegenet objects |
| $<-,genind-method | adegenet formal class (S4) for individual genotypes |
| $<-,genpop-method | adegenet formal class (S4) for allele counts in populations |
| $<-,pdata-method | Accessors for adegenet objects |
| $<-,phylo4-method | Accessors for adegenet objects |
| .genlab | Utilities functions for adegenet |
| .readExt | Utilities functions for adegenet |
| .rmspaces | Utilities functions for adegenet |
| .valid.genind | adegenet formal class (S4) for individual genotypes |
| adegenet | The adegenet package |
| adegenetWeb | Utilities functions for adegenet |
| as.genind | genind constructor |
| as.genpop | genpop constructor |
| callOrNULL-class | Virtual classes for adegenet |
| charOrNULL-class | Virtual classes for adegenet |
| chooseCN | Function to choose a connection network |
| coords.monmonier | Returns original points in results paths of an object of class 'monmonier' |
| df2genind | Convert a data.frame of genotypes to a genind object, and conversely. |
| dist,genpop,ANY,ANY,ANY,missing-method | adegenet formal class (S4) for allele counts in populations |
| dist.genpop | Genetic distances between populations |
| factorOrNULL-class | Virtual classes for adegenet |
| gen-class | Virtual classes for adegenet |
| genind | genind constructor |
| genind-class | adegenet formal class (S4) for individual genotypes |
| genind-methods | genind constructor |
| genind2df | Convert a data.frame of genotypes to a genind object, and conversely. |
| genind2genotype | Conversion functions from adegenet to other R packages |
| genind2genpop | Conversion from a genind to a genpop object |
| genind2hierfstat | Conversion functions from adegenet to other R packages |
| genpop | genpop constructor |
| genpop-class | adegenet formal class (S4) for allele counts in populations |
| genpop-methods | genpop constructor |
| global.rtest | Global and local tests |
| gstat.randtest | Goudet's G-statistic Monte Carlo test for genind object |
| HWE.test.genind | Hardy-Weinberg Equilibrium test for multilocus data |
| hybridize | Simulated hybridization between two samples of populations |
| import2genind | Importing data from several softwares to a genind object |
| indInfo-class | Virtual classes for adegenet |
| intOrNum-class | Virtual classes for adegenet |
| is.genind | genind constructor |
| is.genpop | genpop constructor |
| listOrNULL-class | Virtual classes for adegenet |
| local.rtest | Global and local tests |
| makefreq | Function to generate allelic frequencies |
| microbov | Microsatellites genotypes of 15 cattle breeds |
| monmonier | Boundary detection using Monmonier algorithm |
| na.replace | Replace missing values (NA) from an object |
| na.replace,genind-method | Replace missing values (NA) from an object |
| na.replace,genpop-method | Replace missing values (NA) from an object |
| na.replace-methods | Replace missing values (NA) from an object |
| names,genind-method | adegenet formal class (S4) for individual genotypes |
| names,genpop-method | adegenet formal class (S4) for allele counts in populations |
| nancycats | Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France) |
| old2new | Convert objects with obsolete classe into new objects |
| old2new,ANY-method | Convert objects with obsolete classe into new objects |
| old2new,genind-method | Convert objects with obsolete classe into new objects |
| old2new,genpop-method | Convert objects with obsolete classe into new objects |
| old2new-methods | Convert objects with obsolete classe into new objects |
| optimize.monmonier | Boundary detection using Monmonier algorithm |
| plot.monmonier | Boundary detection using Monmonier algorithm |
| plot.spca | Spatial principal component analysis |
| popInfo-class | Virtual classes for adegenet |
| print,genind-method | adegenet formal class (S4) for individual genotypes |
| print.monmonier | Boundary detection using Monmonier algorithm |
| print.spca | Spatial principal component analysis |
| read.fstat | Reading data from Fstat |
| read.genepop | Reading data from Genepop |
| read.genetix | Reading data from GENETIX |
| read.structure | Reading data from STRUCTURE |
| repool | Pool several genotypes into the same dataset |
| screeplot.spca | Spatial principal component analysis |
| seploc | Separate data per locus |
| seploc,ANY-method | Separate data per locus |
| seploc,genind-method | Separate data per locus |
| seploc,genpop-method | Separate data per locus |
| seploc-methods | Separate data per locus |
| seppop | Separate genotypes per population |
| seppop,ANY-method | Separate genotypes per population |
| seppop,genind-method | Separate genotypes per population |
| seppop-methods | Separate genotypes per population |
| show,genind-method | adegenet formal class (S4) for individual genotypes |
| show,genpop-method | adegenet formal class (S4) for allele counts in populations |
| sim2pop | Simulated genotypes of two georeferenced populations |
| spca | Spatial principal component analysis |
| spcaIllus | Simulated data illustrating the sPCA |
| summary,genind-method | adegenet formal class (S4) for individual genotypes |
| summary,genpop-method | adegenet formal class (S4) for allele counts in populations |
| summary.spca | Spatial principal component analysis |
| truenames | Restore true labels of an object |
| truenames,ANY-method | Restore true labels of an object |
| truenames,genind-method | Restore true labels of an object |
| truenames,genpop-method | Restore true labels of an object |
| truenames-methods | Restore true labels of an object |
| [,genind-method | Accessors for adegenet objects |
| [,genpop-method | Accessors for adegenet objects |