R package with classes and methods to create and manipulate spatial data
sp is an R package that provides classes and methods for spatial data. Spatial data are stored as "sp objects". The classes document where the spatial location information resides. Those include points, lines, polygons (rings, no topology), and grids (pixel/grid). They are defined by a bounding box and a coordinate reference system and can contain attribute data. Utility functions are provided for plotting data as maps, spatial selections, retrieving coordinates, for subsetting, and more. One of the is strengths is the interoperability with other R spatial analysis packages.
For an excellent introduction see Applied Spatial Data Analysis with R.