Spanish R user and solar energy lecturer Oscar Perpiñán Lamigueiro has written a detailed three-part guide to creating beautiful maps and choropleths (maps color-coded with regional data) using the R language. Motivated by the desire to recreate this graphic from the New York Times, Oscar describes how he creates similar high-quality maps using R.
In Part 1, Oscar grabbed some voting data from Spanish elections and shapefiles (detailed map coordinates) from Spain's Official Statistics department (INE) and set to work in R. He then used the maptools package and lattice graphics to create this choropleth of voting patterns in Spain:
In Part 2, he uses the raster package to import pixel-based environmental data from NASA, to create a map that combines population density, land use and land cover in a single map. (Personally, I find it very difficult to interpret such multivariate maps encoded in multiple dimensions of color, but the process is interesting.)
With these examples, you can see how you can get close to the types of maps featured in the New York Times (which, themselves, often involve R in their production). You can find the data and R code used to create these maps at Oscar's blog linked below.
Omnia sunt Communia!: Maps with R (III)