R statistics

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High quality statistic analysis in GRASS GIS is possible thanks to an interface to the most powerful statistics analysis package around: R (http://www.r-project.org).

There is support for:

  • The spgrass6 R addon package provides a convenient R ←→ GRASS GIS 6 interface
  • The rgrass7 R addon package provides a convenient R ←→ GRASS GIS 7 interface

Using R in GRASS GIS directly can has two meanings:

  • The first is that R is run "on top of" GRASS, transferring GRASS data to R to run statistical functions on the imported data as R objects in memory, and possibly transfer the results back to GRASS.
  • The second is to leave the data mostly in GRASS, and to use R as a scripting language "on top of" GRASS with execGRASS() - in this case, little data is moved to R, so memory constraints are not important, but R functionality is available.

Overview

Installation

See R_statistics/Installation

Command help

Start the R help browser:

help.start()
  • GRASS GIS 6: Select the Packages entry and then spgrass6.
  • GRASS GIS 7: Select the Packages entry and then rgrass7.

Using R within a GRASS GIS session

Using GRASS GIS functionality within a R session

To call GRASS functionality from R, use the initGRASS() function to define the GRASS settings:

   library(spgrass6)
   
   # initialisation and the use of spearfish60 data
   initGRASS(gisBase = "/usr/local/grass-6.4.1", home = tempdir(), 
             gisDbase = "/home/neteler/grassdata/",
             location = "spearfish60", mapset = "user1", SG="elevation.dem",
             override = TRUE)
   
   system("g.region -d")
   # verify
   gmeta6()
   
   spear <- readRAST6(c("geology", "elevation.dem"),
             cat=c(TRUE, FALSE), ignore.stderr=TRUE,
             plugin=NULL)
   
   summary(spear$geology)

Run this script with

   R CMD BATCH batch.R

The result is (shorted here):

   cat batch.Rout
   
   R version 2.10.0 (2009-10-26)
   Copyright (C) 2009 The R Foundation for Statistical Computing
   ISBN 3-900051-07-0
   ...
   > library(spgrass6)
   Loading required package: sp
   Loading required package: rgdal
   Geospatial Data Abstraction Library extensions to R successfully loaded
   Loaded GDAL runtime: GDAL 1.7.2, released 2010/04/23
   Path to GDAL shared files: /usr/local/share/gdal
   Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009
   Path to PROJ.4 shared files: (autodetected)
   Loading required package: XML
   GRASS GIS interface loaded with GRASS version: (GRASS not running)
   > 
   > # initialisation and the use of spearfish60 data
   > initGRASS(gisBase = "/usr/local/grass-6.4.1", home = tempdir(), gisDbase = "/home/neteler/grassdata/",
   +           location = "spearfish60", mapset = "user1", SG="elevation.dem", override = TRUE)
   gisdbase    /home/neteler/grassdata/ 
   location    spearfish60 
   mapset      user1 
   rows        477 
   columns     634 
   north       4928010 
   south       4913700 
   west        589980 
   east        609000 
   nsres       30 
   ewres       30 
   projection  +proj=utm +zone=13 +a=6378206.4 +rf=294.9786982 +no_defs
   +nadgrids=/usr/local/grass-6.4.1/etc/nad/conus +to_meter=1.0 
   Warning messages:
   1: In dir.create(gisDbase) : '/home/neteler/grassdata' already exists
   2: In dir.create(loc_path) :
     '/home/neteler/grassdata//spearfish60' already exists
   > 
   > system("g.region -d")
   > # verify
   > gmeta6()
   gisdbase    /home/neteler/grassdata/ 
   location    spearfish60 
   mapset      user1 
   rows        477 
   columns     634 
   north       4928010 
   ...
   > 
   > spear <- readRAST6(c("geology", "elevation.dem"),
   +           cat=c(TRUE, FALSE), ignore.stderr=TRUE,
   +           plugin=NULL)
   > 
   > summary(spear$geology)
   metamorphic  transition     igneous   sandstone   limestone       shale 
         11693         142       36534       74959       61355       46423 
   sandy shale    claysand        sand        NA's 
         11266       14535       36561        8950 
   > 
   > 
   > proc.time()
      user  system elapsed 
     2.891   0.492   3.412 


Getting Support

  • Primary support for R + GRASS and the spgrass6 package is through the grass-stats mailing list.

See also

  • Using R and GRASS with cygwin: It is possible to use Rterm inside the GRASS shell in cygwin, just as in Unix/Linux or OSX. You should not, however, start Rterm from a cygwin xterm, because Rterm is not expecting to be run in an xterm under Windows, and loses its input. If you use the regular cygwin bash shell, but need to start display windows, start X from within GRASS with startx &, and then start Rterm in the same cygwin shell, not in the xterm.
  • Spatial data in R (sp) is a R library that provides classes and methods for spatial data (points, lines, polygons, grids), and to new or existing spatial statistics R packages that use sp, depend on sp, or will become dependent on sp, such as maptools, rgdal, splancs, spgrass6, gstat, spgwr and many others.
  • RPy - Python interface to the R Programming Language

Open tickets

  • Ticket trac #1103 (new enhancement) WinGrass64 - windows-commandline not released: a Grass-session with wxGui, command-line and R inside a Grass-session would be possible (as already does in WinGrass7)

Workshop material

Articles

  • GRASS News vol.3, June 2005 (R. Bivand. Interfacing GRASS 6 and R. GRASS Newsletter, 3:11-16, June 2005. ISSN 1614-8746).
  • OSGeo Journal vol. 1 May 2007 (R. Bivand. Using the R— GRASS interface. OSGeo Journal, 1:31-33, May 2007. ISSN 1614-8746).
  • GRASS Book, last chapter