R is an open source statistical programming language and platform that is widely used in statistical analysis, data science and data visualization. Although R was not originally designed to work with spatial data formats, it has long had a strong geospatial developer community and can be used as a powerful GIS platform with the addition of external packages. R is particularly powerful for spatial statistical analysis and quantitative researchers in particular may find R more useful than GIS desktop applications.
R is free and and cross-platform and can be downloaded from The Comprehensive R Archive Network (CRAN).
Most users work with R in an IDE. We recommend RStudio, which has a free desktop version that you can download here.
You will surely need to install at least a few external packages to work with geospatial data. We will list here a number of the most useful packages, but there are many others. A better idea may be to see the excellent CRAN Task View: Analysis of Spatial Data for a longer and more detailed list of geospatial packages
Basic data manipulation
raster for working with raster (gridded) data.
rgdal provides bindings to the Geospatial Data Abstraction Library
rgeos for manipulation and querying of spatial geometries using the GEOS geometry engine
maptools is a popular set of tools for manipulating geographic data
shapefiles has functions for reading and writing ESRI Shapefiles
ncdf4 for working with netCDF files
Cartography and data visualization
ggplot2 for crating plots and maps using the "grammar of graphics"
viridis is another popular source for color palettes
tmap for thematic mapping using "grammar of graphics" syntax
mapview for creation of interactive spatial visualizations with pop-up windows for attribute data
cartography for creation of cartographic representations with typical map elements
choroplethr simplifies the production of choropleth maps
ggmap web mapping with Google Maps of OpenStreetMap
spatial package for kriging and point pattern analysis
spatstat package for point pattern analysis
gstat package for modelling, prediction and simulation of geostatistical data in one, two or three dimensions
spdep for creating spatial weights matrices
tigris provides cartographic files from the US Census
tidycensus access to the US Census APIs for the American Community Survey and then Decennial Census