A C D F G H I K L M N O P R S T misc
adegenet-package | The adegenet package |
$,genind-method | Accessors for adegenet objects |
$,genpop-method | Accessors for adegenet objects |
$<-,genind-method | Accessors for adegenet objects |
$<-,genpop-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 |
adegenetTutorial | Utilities functions for adegenet |
adegenetWeb | Utilities functions for adegenet |
as,genind,data.frame-method | Converting genind/genpop objects to other classes |
as,genind,genpop-method | Converting genind/genpop objects to other classes |
as,genind,ktab-method | Converting genind/genpop objects to other classes |
as,genind,matrix-method | Converting genind/genpop objects to other classes |
as,genpop,data.frame-method | Converting genind/genpop objects to other classes |
as,genpop,ktab-method | Converting genind/genpop objects to other classes |
as,genpop,matrix-method | Converting genind/genpop objects to other classes |
as-method | Converting genind/genpop objects to other classes |
as.data.frame.genind | Converting genind/genpop objects to other classes |
as.data.frame.genpop | Converting genind/genpop objects to other classes |
as.genind | genind constructor |
as.genpop | genpop constructor |
as.genpop.genind | Converting genind/genpop objects to other classes |
as.ktab.genind | Converting genind/genpop objects to other classes |
as.ktab.genpop | Converting genind/genpop objects to other classes |
as.matrix.genind | Converting genind/genpop objects to other classes |
as.matrix.genpop | Converting genind/genpop objects to other classes |
callOrNULL-class | Virtual classes for adegenet |
charOrNULL-class | Virtual classes for adegenet |
chooseCN | Function to choose a connection network |
coerce,genind,data.frame-method | Converting genind/genpop objects to other classes |
coerce,genind,genpop-method | Converting genind/genpop objects to other classes |
coerce,genind,ktab-method | Converting genind/genpop objects to other classes |
coerce,genind,matrix-method | Converting genind/genpop objects to other classes |
coerce,genpop,data.frame-method | Converting genind/genpop objects to other classes |
coerce,genpop,ktab-method | Converting genind/genpop objects to other classes |
coerce,genpop,matrix-method | Converting genind/genpop objects to other classes |
colorplot | Represents a cloud of points with colors |
colorplot.spca | Spatial principal component analysis |
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 |
fstat | F statistics for genind objects |
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 |
ktab-class | Converting genind/genpop objects to other classes |
listOrNULL-class | Virtual classes for adegenet |
loadingplot | Represents a cloud of points with colors |
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) |
nLoc | adegenet formal class (S4) for individual genotypes |
nLoc,genind-method | adegenet formal class (S4) for individual genotypes |
nLoc,genpop-method | adegenet formal class (S4) for allele counts in populations |
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 |
propShared | Compute proportion of shared alleles |
propTyped | Compute the proportion of typed elements |
propTyped,genind-method | Compute the proportion of typed elements |
propTyped,genpop-method | Compute the proportion of typed elements |
propTyped-methods | 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.structure | Reading data from STRUCTURE |
repool | Pool several genotypes into the same dataset |
rupica | Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France) |
scaleGen | Compute scaled allele frequencies |
scaleGen,genind-method | Compute scaled allele frequencies |
scaleGen,genpop-method | Compute scaled allele frequencies |
scaleGen-methods | Compute scaled allele frequencies |
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 |