Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
This wiki is dedicated to the development of adegenet. It is relevant for developers of the package, developers of other packages depending on adegenet, and for users who want to be using the latest features as well.
The adegenet website is available at http://adegenet.r-forge.r-project.org/.
The following sections are available: