Entry: HWE.test.genind
Aliases: HWE.test.genind
Keywords: manip multivariate
Description: Hardy-Weinberg Equilibrium test for multilocus data
URL: ../../../library/adegenet/html/HWE.html

Entry: Accessors
Aliases: $,genind-method $,genpop-method $<-,genind-method $<-,genpop-method [,genind-method [,genpop-method nLoc nLoc,genind-method nLoc,genpop-method pop pop<- pop,genind-method pop<-,genind-method locNames locNames,genind-method locNames,genpop-method
Keywords: manip
Description: Accessors for adegenet objects
URL: ../../../library/adegenet/html/accessors.html

Entry: adegenet-package
Aliases: adegenet-package adegenet
Keywords: manip multivariate
Description: The adegenet package
URL: ../../../library/adegenet/html/adegenet.package.html

Entry: as methods in adegenet
Aliases: as-method as,genind,data.frame-method as,genpop,data.frame-method as,genind,matrix-method as,genpop,matrix-method as,genind,genpop-method ktab-class as,genind,ktab-method as,genpop,ktab-method coerce,genind,data.frame-method coerce,genpop,data.frame-method coerce,genind,matrix-method coerce,genpop,matrix-method coerce,genind,genpop-method coerce,genind,ktab-method coerce,genpop,ktab-method as.data.frame.genind as.data.frame.genpop as.matrix.genind as.matrix.genpop as.genpop.genind as.ktab.genind as.ktab.genpop
Keywords: methods
Description: Converting genind/genpop objects to other classes
URL: ../../../library/adegenet/html/as-methods.html

Entry: genind constructor
Aliases: genind-methods genind as.genind is.genind
Keywords: manip
Description: genind constructor
URL: ../../../library/adegenet/html/as.genind.html

Entry: genpop constructor
Aliases: genpop-methods genpop as.genpop is.genpop
Keywords: manip
Description: genpop constructor
URL: ../../../library/adegenet/html/as.genpop.html

Entry: Auxiliary functions
Aliases: adegenetWeb adegenetTutorial checkType .rmspaces .genlab .readExt
Keywords: manip
Description: Utilities functions for adegenet
URL: ../../../library/adegenet/html/auxil.html

Entry: chooseCN
Aliases: chooseCN
Keywords: spatial utilities
Description: Function to choose a connection network
URL: ../../../library/adegenet/html/chooseCN.html

Entry: colorplot
Aliases: colorplot colorplot.default
Keywords: multivariate hplot
Description: Represents a cloud of points with colors
URL: ../../../library/adegenet/html/colorplot.html

Entry: coords.monmonier
Aliases: coords.monmonier
Keywords: methods manip
Description: Returns original points in results paths of an object of class 'monmonier'
URL: ../../../library/adegenet/html/coords.monmonier.html

Entry: df2genind
Aliases: df2genind genind2df
Keywords: manip
Description: Convert a data.frame of genotypes to a genind object, and conversely.
URL: ../../../library/adegenet/html/df2genind.html

Entry: dist.genpop
Aliases: dist.genpop
Keywords: multivariate
Description: Genetic distances between populations
URL: ../../../library/adegenet/html/dist.genpop.html

Entry: export
Aliases: genind2genotype genind2hierfstat
Keywords: manip
Description: Conversion functions from adegenet to other R packages
URL: ../../../library/adegenet/html/export.html

Entry: fstat
Aliases: fstat
Keywords: multivariate
Description: F statistics for genind objects
URL: ../../../library/adegenet/html/fstat.html

Entry: genind
Aliases: genind-class print,genind-method show,genind-method names,genind-method summary,genind-method .valid.genind
Keywords: classes manip multivariate
Description: adegenet formal class (S4) for individual genotypes
URL: ../../../library/adegenet/html/genind.html

Entry: genind2genpop
Aliases: genind2genpop
Keywords: classes manip multivariate
Description: Conversion from a genind to a genpop object
URL: ../../../library/adegenet/html/genind2genpop.html

Entry: genpop
Aliases: genpop-class dist,genpop,ANY,ANY,ANY,missing-method names,genpop-method show,genpop-method summary,genpop-method
Keywords: classes manip multivariate
Description: adegenet formal class (S4) for allele counts in populations
URL: ../../../library/adegenet/html/genpop.html

Entry: gstat.randtest
Aliases: gstat.randtest
Keywords: manip multivariate
Description: Goudet's G-statistic Monte Carlo test for genind object
URL: ../../../library/adegenet/html/gstat.randtest.html

Entry: hybridize
Aliases: hybridize
Keywords: manip
Description: Simulated hybridization between two samples of populations
URL: ../../../library/adegenet/html/hybridize.html

Entry: import
Aliases: import2genind import2genind
Keywords: manip
Description: Importing data from several softwares to a genind object
URL: ../../../library/adegenet/html/import.html

Entry: isPoly-methods
Aliases: isPoly isPoly-methods isPoly,genind-method isPoly,genpop-method
Keywords: methods manip
Description: Assess polymorphism in genind/genpop objects
URL: ../../../library/adegenet/html/isPoly.html

Entry: loadingplot
Aliases: loadingplot loadingplot.default
Keywords: multivariate hplot
Description: Represents a cloud of points with colors
URL: ../../../library/adegenet/html/loadingplot.html

Entry: makefreq
Aliases: makefreq
Keywords: manip multivariate
Description: Function to generate allelic frequencies
URL: ../../../library/adegenet/html/makefreq.html

Entry: microbov
Aliases: microbov
Keywords: datasets
Description: Microsatellites genotypes of 15 cattle breeds
URL: ../../../library/adegenet/html/microbov.html

Entry: monmonier
Aliases: monmonier optimize.monmonier plot.monmonier print.monmonier
Keywords: multivariate spatial
Description: Boundary detection using Monmonier algorithm
URL: ../../../library/adegenet/html/monmonier.html

Entry: na.replace-methods
Aliases: na.replace na.replace-methods na.replace,genind-method na.replace,genpop-method
Keywords: methods manip
Description: Replace missing values (NA) from an object
URL: ../../../library/adegenet/html/na.replace.html

Entry: nancycats
Aliases: nancycats
Keywords: datasets
Description: Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
URL: ../../../library/adegenet/html/nancycats.html

Entry: old2new
Aliases: old2new old2new,ANY-method old2new-methods old2new,genind-method old2new,genpop-method
Keywords: methods classes manip
Description: Convert objects with obsolete classe into new objects
URL: ../../../library/adegenet/html/old2new.html

Entry: propShared
Aliases: propShared
Keywords: manip multivariate
Description: Compute proportion of shared alleles
URL: ../../../library/adegenet/html/propShared.html

Entry: propTyped-methods
Aliases: propTyped propTyped-methods propTyped,genind-method propTyped,genpop-method
Keywords: methods manip
Description: Compute the proportion of typed elements
URL: ../../../library/adegenet/html/propTyped.html

Entry: read.fstat
Aliases: read.fstat
Keywords: manip
Description: Reading data from Fstat
URL: ../../../library/adegenet/html/read.fstat.html

Entry: read.genepop
Aliases: read.genepop
Keywords: manip
Description: Reading data from Genepop
URL: ../../../library/adegenet/html/read.genepop.html

Entry: read.genetix
Aliases: read.genetix
Keywords: manip
Description: Reading data from GENETIX
URL: ../../../library/adegenet/html/read.genetix.html

Entry: read.structure
Aliases: read.structure
Keywords: manip
Description: Reading data from STRUCTURE
URL: ../../../library/adegenet/html/read.structure.html

Entry: repool
Aliases: repool
Keywords: manip
Description: Pool several genotypes into the same dataset
URL: ../../../library/adegenet/html/repool.html

Entry: rupica
Aliases: rupica
Keywords: datasets
Description: Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France)
URL: ../../../library/adegenet/html/rupica.html

Entry: scaleGen-methods
Aliases: scaleGen scaleGen-methods scaleGen,genind-method scaleGen,genpop-method
Keywords: methods manip
Description: Compute scaled allele frequencies
URL: ../../../library/adegenet/html/scale.html

Entry: selPopSize
Aliases: selPopSize selPopSize-methods selPopSize,ANY-method selPopSize,genind-method
Keywords: manip
Description: Select genotypes of well-represented populations
URL: ../../../library/adegenet/html/selpopsize.html

Entry: seploc
Aliases: seploc seploc-methods seploc,ANY-method seploc,genind-method seploc,genpop-method
Keywords: manip
Description: Separate data per locus
URL: ../../../library/adegenet/html/seploc.html

Entry: seppop
Aliases: seppop seppop-methods seppop,ANY-method seppop,genind-method
Keywords: manip
Description: Separate genotypes per population
URL: ../../../library/adegenet/html/seppop.html

Entry: SequencesToGenind
Aliases: DNAbin2genind
Keywords: manip
Description: Importing data from an alignement of sequences to a genind object
URL: ../../../library/adegenet/html/sequences.html

Entry: sim2pop
Aliases: sim2pop
Keywords: datasets
Description: Simulated genotypes of two georeferenced populations
URL: ../../../library/adegenet/html/sim2pop.html

Entry: spca
Aliases: spca print.spca summary.spca plot.spca screeplot.spca colorplot.spca
Keywords: spatial multivariate
Description: Spatial principal component analysis
URL: ../../../library/adegenet/html/spca.html

Entry: global.rtest
Aliases: global.rtest local.rtest
Keywords: multivariate spatial
Description: Global and local tests
URL: ../../../library/adegenet/html/spca.rtests.html

Entry: spcaIllus
Aliases: spcaIllus
Keywords: datasets spatial
Description: Simulated data illustrating the sPCA
URL: ../../../library/adegenet/html/spcaIllus.html

Entry: truenames
Aliases: truenames truenames-methods truenames,ANY-method truenames,genind-method truenames,genpop-method
Keywords: manip
Description: Restore true labels of an object
URL: ../../../library/adegenet/html/truenames.html

Entry: virtualClasses
Aliases: indInfo-class popInfo-class gen-class callOrNULL-class charOrNULL-class factorOrNULL-class intOrNum-class listOrNULL-class
Keywords: classes
Description: Virtual classes for adegenet
URL: ../../../library/adegenet/html/virClasses.html
