In rsbivand/rgrass7: Interface Between 'GRASS' Geographical Information System and 'R'
knitr::opts_chunk$set(message = FALSE, warning = FALSE)
Introduction
The original R-GRASS interface [@bivand:00; @neteler+mitasova:08] was written mainly to permit R objects represented as sp class objects to be moved to GRASS, and GRASS objects to be moved to R for statistical analysis. From spgrass6 0.6-3 (April 2009) following a fruitful workshop at Queen's University, Belfast, the interface was re-written to use the --interface-description flag provided for each GRASS command, also used by the Python interface to GRASS commands. Command interface descriptions are parsed from XML and cached as R objects for efficiency. The current version of the R-GRASS interface is contained in this package, rgrass. In addition, an R function initGRASS() was written to permit GRASS to be started from within GRASS to which we will return below.
Starting R inside GRASS
When starting GRASS GIS from a terminal console (here GRASS 8.3.2), one can continue in the GRASS terminal console, starting an interactive R session from there (here R 4.3.3). Loading and attaching the R-GRASS interface package rgrass in the R session, we see that the current GRASS location is detected and reported:
$ grass
Starting GRASS GIS...
__________ ___ __________ _______________
/ ____/ __ \/ | / ___/ ___/ / ____/ _/ ___/
/ / __/ /_/ / /| | \__ \\_ \ / / __ / / \__ \
/ /_/ / _, _/ ___ |___/ /__/ / / /_/ // / ___/ /
\____/_/ |_/_/ |_/____/____/ \____/___//____/
Welcome to GRASS GIS 8.3.2
GRASS GIS homepage: https://grass.osgeo.org
This version running through: Bash Shell (/bin/bash)
Help is available with the command: g.manual -i
See the licence terms with: g.version -c
See citation options with: g.version -x
If required, restart the GUI with: g.gui wxpython
When ready to quit enter: exit
Launching <wxpython> GUI in the background, please wait...
GRASS nc_basic_spm_grass7/rsb:~ > R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...
> library(rgrass)
GRASS GIS interface loaded with GRASS version: GRASS 8.3.2 (2024)
and location: nc_basic_spm_grass7
Since rgrass knows the current location, we can for example use execGRASS() to list GRASS rasters in the PERMANENT mapset in the standard North Carolina basic data set (https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.zip):
> execGRASS("g.list", type="raster", mapset="PERMANENT")
basins
elevation
elevation_shade
geology
lakes
landuse
soils
> q()
Save workspace image? [y/n/c]: n
GRASS nc_basic_spm_grass7/rsb:github-rsb > exit
exit
Done.
Goodbye from GRASS GIS
Leaving R returns us to the GRASS terminal console, which we can also exit.
R can also be started within the GRASS GUI, by choosing the console tab, and entering for example rstudio, or another R graphical user interface. This screendump shows the same listing of rasters in PERMANENT in rstudio:
knitr::include_graphics("rstudio_in_GRASS.png")
Starting GRASS inside R
From spgrass6 0.6-3, it has also been possible to start a GRASS session from a running R session using the initGRASS() function. This is done by setting GRASS and environment variables from the R session (https://grass.osgeo.org/grass-stable/manuals/variables.html).
It may be useful to set an environment variable to the value of GISBASE, as shown for example in the GRASS terminal console:
GRASS nc_basic_spm_grass7/rsb:github-rsb > echo $GISBASE
/home/rsb/topics/grass/g832/grass83
Starting R with such a suitable environment variable set lets us retrieve it later when needed. When loaded and attached, rgrass reports that it seems that GRASS is not running:
$ GRASS_INSTALLATION=/home/rsb/topics/grass/g832/grass83 R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...
> library(rgrass)
GRASS GIS interface loaded with GRASS version: GRASS 8.3.2 (2024)
and location: nc_basic_spm_grass7
On Windows, if GRASS was installed through the OSGeo4W installer, the R session must be started in the OSGeo4W shell, including starting RStudio. In using the OSGeo4W shell, found in the Windows left app navbar (for example here in the QGIS app group, also found in the OSGeo4W app group):
knitr::include_graphics("OSGeo4W_QGIS_navbar.png")
note that the standard PATH to Rgui or RStudio apps is overwritten, so the program name has to be entered with its full path, for example "C:\Program Files\R\R-4.3.3\bin\x64\Rgui.exe" or "C:\Program Files\RStudio\rstudio.exe" in quotes because of the space. In addition, the working directory in not user-writeable, so also needs to be changed when using Rgui, while RStudio itself changes to the directory Windows treats as your home directory. First Rgui:
knitr::include_graphics("OSGeo4W_Rgui.png")
and RStudio:
knitr::include_graphics("OSGeo4W_rstudio.png")
In both cases, warnings can be seen on loading terra which are not associated with RStudio, Rgui or R, but in this case were caused by the OSGeo4W express installer not installing the correct plugins for the GDAL version it installed by default. Using the OSGeo4W custom installer from OSGeo4W Setup (also in the left app navbar), the latest version of GDAL can be installed, resolving the non-critical warnings.
If not started in the OSGeo4W shell, the non-standard placing of files and of environment variables confuses the function and initGRASS will exit with an error before confusion leads to further errors. For further details, see https://github.com/rsbivand/rgrass/issues/16 and https://lists.osgeo.org/pipermail/grass-stats/2018-November/001800.html.
The same restriction applies to use of GRASS with QGIS Windows standalone installations, which may be used with initGRASS only if the R session is started from the OSGeo4W shell shipped as part of the standalone installer (see https://github.com/rsbivand/rgrass/issues/87).
The QGIS Windows standalone installer may be used to install GRASS for rgrass, but if GRASS is to be run within R, again R or RStudio must be started in the OSGeo4W shell installed this time by the QGIS Windows standalone installer:
knitr::include_graphics("OSGeo4W_QGIS_Rgui.png")
If not started from the required OSGeo4W shell, the function will exit with an error before confusion leads to further errors.
knitr::include_graphics("OSGeo4W_QGIS_rstudio.png")
Starting GRASS from R may use a temporary or an existing GRASS LOCATION, as has already been demonstrated in the temporary directory case in the OSGeo4W and QGIS standalone installer cases.
Temporary GRASS location
If we don't pass an existing location to initGRASS(), a temporary GRASS location will be created and set.
Here we'll use a raster file provided with terra:
> library(terra)
terra 1.7.71
> f <- system.file("ex/elev.tif", package="terra")
> r <- rast(f)
The first argument to initGRASS() is gisBase=, which here we are passing the value of the environment variable after checking that it is a directory. The second argument is where to write the GISRC file. The third is a template raster (here a "SpatRaster" object) from which to clone the temporary location size, position, resolution and projection:
> GRASS_INSTALLATION <- Sys.getenv("GRASS_INSTALLATION")
> file.info(GRASS_INSTALLATION)$isdir
[1] TRUE
> loc <- initGRASS(gisBase=GRASS_INSTALLATION, home=tempdir(), SG=r, override=TRUE)
If the gisBase argument is missing, initGRASS() will do a minimal effort of guessing it.
Firstly, if a GRASS_INSTALLATION environment variable is availabe, then its value will automatically be used for gisBase.
If not, then the system command grass --config path will be tried to get the value of GISBASE that corresponds to the GRASS installation in the system PATH (if any).
As can be seen, initGRASS() creates not only environment and GRASS variables, but also many files in the location mapsets; g.gisenv also shows details:
> list.files(file.path(loc$GISDBASE, loc$LOCATION_NAME), recursive=TRUE)
[1] "file28aaf6dc1c44c/WIND" "file28aaf6dc1c44c/windows/input"
[3] "PERMANENT/DEFAULT_WIND" "PERMANENT/PROJ_EPSG"
[5] "PERMANENT/PROJ_INFO" "PERMANENT/PROJ_SRID"
[7] "PERMANENT/PROJ_UNITS" "PERMANENT/PROJ_WKT"
[9] "PERMANENT/WIND"
> execGRASS("g.gisenv")
GISDBASE='/tmp/Rtmpe7QdVd';
LOCATION_NAME='file28aaf5be4b905';
MAPSET='file28aaf6dc1c44c';
GRASS_GUI='text';
We may now write R objects to the temporary GRASS location for manipulation and analysis, here calculating slope and aspect layers:
> write_RAST(r, vname="terra_elev")
Importing raster map <terra_elev>...
100%
SpatRaster read into GRASS using r.in.gdal from file
> execGRASS("g.list", type="raster", mapset=loc$MAPSET)
terra_elev
> execGRASS("r.slope.aspect", flags="overwrite", elevation="terra_elev", slope="slope", aspect="aspect")
100%
Aspect raster map <aspect> complete
Slope raster map <slope> complete
> u1 <- read_RAST(c("terra_elev", "slope", "aspect"))
Checking GDAL data type and nodata value...
100%
Using GDAL data type <UInt16>
Exporting raster data to RRASTER format...
100%
r.out.gdal complete. File </tmp/RtmpLsAbI6/file29f4b33cd20f6.grd> created.
Checking GDAL data type and nodata value...
100%
Using GDAL data type <Float32>
Exporting raster data to RRASTER format...
100%
r.out.gdal complete. File </tmp/RtmpLsAbI6/file29f4b2d2e045b.grd> created.
Checking GDAL data type and nodata value...
100%
Using GDAL data type <Float32>
Exporting raster data to RRASTER format...
100%
r.out.gdal complete. File </tmp/RtmpLsAbI6/file29f4b52cab445.grd> created.
> u1
class : SpatRaster
dimensions : 90, 95, 3 (nrow, ncol, nlyr)
resolution : 0.008333326, 0.008333333 (x, y)
extent : 5.741667, 6.533333, 49.44167, 50.19167 (xmin, xmax, ymin, ymax)
coord. ref. : lon/lat WGS 84 (EPSG:4326)
sources : file29f4b33cd20f6.grd
file29f4b2d2e045b.grd
file29f4b52cab445.grd
names : terra_elev, slope, aspect
min values : 141.00000000, 0.01416342, 0.08974174
max values : 547.000000, 7.229438, 360.000000
Existing GRASS location
Similarly, GRASS may be started in an R session with an existing location by providing the gisDbase=, location= and mapset= arguments with valid values:
$ GRASS_INSTALLATION=/home/rsb/topics/grass/g832/grass83 R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...
> library(rgrass)
GRASS GIS interface loaded with GRASS version: (GRASS not running)
> GRASS_INSTALLATION <- Sys.getenv("GRASS_INSTALLATION")
> loc <- initGRASS(GRASS_INSTALLATION, home=tempdir(), gisDbase="/home/rsb/topics/grassdata", location="nc_basic_spm_grass7", mapset="rsb", override=TRUE)
> execGRASS("g.gisenv")
GISDBASE='/home/rsb/topics/grassdata';
LOCATION_NAME='nc_basic_spm_grass7';
MAPSET='rsb';
GRASS_GUI='text';
> execGRASS("g.list", type="raster", mapset="PERMANENT")
basins
elevation
elevation_shade
geology
lakes
landuse
soils
References
rsbivand/rgrass7 documentation built on Nov. 3, 2024, 6:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
knitr::opts_chunk$set(message = FALSE, warning = FALSE)
Introduction
The original R-GRASS interface [@bivand:00; @neteler+mitasova:08] was written mainly to permit R objects represented as sp class objects to be moved to GRASS, and GRASS objects to be moved to R for statistical analysis. From spgrass6 0.6-3 (April 2009) following a fruitful workshop at Queen's University, Belfast, the interface was re-written to use the --interface-description flag provided for each GRASS command, also used by the Python interface to GRASS commands. Command interface descriptions are parsed from XML and cached as R objects for efficiency. The current version of the R-GRASS interface is contained in this package, rgrass. In addition, an R function initGRASS() was written to permit GRASS to be started from within GRASS to which we will return below.
Starting R inside GRASS
When starting GRASS GIS from a terminal console (here GRASS 8.3.2), one can continue in the GRASS terminal console, starting an interactive R session from there (here R 4.3.3). Loading and attaching the R-GRASS interface package rgrass in the R session, we see that the current GRASS location is detected and reported:
$ grass
Starting GRASS GIS...
__________ ___ __________ _______________
/ ____/ __ \/ | / ___/ ___/ / ____/ _/ ___/
/ / __/ /_/ / /| | \__ \\_ \ / / __ / / \__ \
/ /_/ / _, _/ ___ |___/ /__/ / / /_/ // / ___/ /
\____/_/ |_/_/ |_/____/____/ \____/___//____/
Welcome to GRASS GIS 8.3.2
GRASS GIS homepage: https://grass.osgeo.org
This version running through: Bash Shell (/bin/bash)
Help is available with the command: g.manual -i
See the licence terms with: g.version -c
See citation options with: g.version -x
If required, restart the GUI with: g.gui wxpython
When ready to quit enter: exit
Launching <wxpython> GUI in the background, please wait...
GRASS nc_basic_spm_grass7/rsb:~ > R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...
> library(rgrass)
GRASS GIS interface loaded with GRASS version: GRASS 8.3.2 (2024)
and location: nc_basic_spm_grass7
Since rgrass knows the current location, we can for example use execGRASS() to list GRASS rasters in the PERMANENT mapset in the standard North Carolina basic data set (https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.zip):
> execGRASS("g.list", type="raster", mapset="PERMANENT")
basins
elevation
elevation_shade
geology
lakes
landuse
soils
> q()
Save workspace image? [y/n/c]: n
GRASS nc_basic_spm_grass7/rsb:github-rsb > exit
exit
Done.
Goodbye from GRASS GIS
Leaving R returns us to the GRASS terminal console, which we can also exit.
R can also be started within the GRASS GUI, by choosing the console tab, and entering for example rstudio, or another R graphical user interface. This screendump shows the same listing of rasters in PERMANENT in rstudio:
knitr::include_graphics("rstudio_in_GRASS.png")
Starting GRASS inside R
From spgrass6 0.6-3, it has also been possible to start a GRASS session from a running R session using the initGRASS() function. This is done by setting GRASS and environment variables from the R session (https://grass.osgeo.org/grass-stable/manuals/variables.html).
It may be useful to set an environment variable to the value of GISBASE, as shown for example in the GRASS terminal console:
GRASS nc_basic_spm_grass7/rsb:github-rsb > echo $GISBASE /home/rsb/topics/grass/g832/grass83
Starting R with such a suitable environment variable set lets us retrieve it later when needed. When loaded and attached, rgrass reports that it seems that GRASS is not running:
$ GRASS_INSTALLATION=/home/rsb/topics/grass/g832/grass83 R R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) ... > library(rgrass) GRASS GIS interface loaded with GRASS version: GRASS 8.3.2 (2024) and location: nc_basic_spm_grass7
On Windows, if GRASS was installed through the OSGeo4W installer, the R session must be started in the OSGeo4W shell, including starting RStudio. In using the OSGeo4W shell, found in the Windows left app navbar (for example here in the QGIS app group, also found in the OSGeo4W app group):
knitr::include_graphics("OSGeo4W_QGIS_navbar.png")
note that the standard PATH to Rgui or RStudio apps is overwritten, so the program name has to be entered with its full path, for example "C:\Program Files\R\R-4.3.3\bin\x64\Rgui.exe" or "C:\Program Files\RStudio\rstudio.exe" in quotes because of the space. In addition, the working directory in not user-writeable, so also needs to be changed when using Rgui, while RStudio itself changes to the directory Windows treats as your home directory. First Rgui:
knitr::include_graphics("OSGeo4W_Rgui.png")
and RStudio:
knitr::include_graphics("OSGeo4W_rstudio.png")
In both cases, warnings can be seen on loading terra which are not associated with RStudio, Rgui or R, but in this case were caused by the OSGeo4W express installer not installing the correct plugins for the GDAL version it installed by default. Using the OSGeo4W custom installer from OSGeo4W Setup (also in the left app navbar), the latest version of GDAL can be installed, resolving the non-critical warnings.
If not started in the OSGeo4W shell, the non-standard placing of files and of environment variables confuses the function and initGRASS will exit with an error before confusion leads to further errors. For further details, see https://github.com/rsbivand/rgrass/issues/16 and https://lists.osgeo.org/pipermail/grass-stats/2018-November/001800.html.
The same restriction applies to use of GRASS with QGIS Windows standalone installations, which may be used with initGRASS only if the R session is started from the OSGeo4W shell shipped as part of the standalone installer (see https://github.com/rsbivand/rgrass/issues/87).
The QGIS Windows standalone installer may be used to install GRASS for rgrass, but if GRASS is to be run within R, again R or RStudio must be started in the OSGeo4W shell installed this time by the QGIS Windows standalone installer:
knitr::include_graphics("OSGeo4W_QGIS_Rgui.png")
If not started from the required OSGeo4W shell, the function will exit with an error before confusion leads to further errors.
knitr::include_graphics("OSGeo4W_QGIS_rstudio.png")
Starting GRASS from R may use a temporary or an existing GRASS LOCATION, as has already been demonstrated in the temporary directory case in the OSGeo4W and QGIS standalone installer cases.
Temporary GRASS location
If we don't pass an existing location to initGRASS(), a temporary GRASS location will be created and set.
Here we'll use a raster file provided with terra:
> library(terra) terra 1.7.71 > f <- system.file("ex/elev.tif", package="terra") > r <- rast(f)
The first argument to initGRASS() is gisBase=, which here we are passing the value of the environment variable after checking that it is a directory. The second argument is where to write the GISRC file. The third is a template raster (here a "SpatRaster" object) from which to clone the temporary location size, position, resolution and projection:
> GRASS_INSTALLATION <- Sys.getenv("GRASS_INSTALLATION") > file.info(GRASS_INSTALLATION)$isdir [1] TRUE > loc <- initGRASS(gisBase=GRASS_INSTALLATION, home=tempdir(), SG=r, override=TRUE)
If the gisBase argument is missing, initGRASS() will do a minimal effort of guessing it.
Firstly, if a GRASS_INSTALLATION environment variable is availabe, then its value will automatically be used for gisBase.
If not, then the system command grass --config path will be tried to get the value of GISBASE that corresponds to the GRASS installation in the system PATH (if any).
As can be seen, initGRASS() creates not only environment and GRASS variables, but also many files in the location mapsets; g.gisenv also shows details:
> list.files(file.path(loc$GISDBASE, loc$LOCATION_NAME), recursive=TRUE)
[1] "file28aaf6dc1c44c/WIND" "file28aaf6dc1c44c/windows/input"
[3] "PERMANENT/DEFAULT_WIND" "PERMANENT/PROJ_EPSG"
[5] "PERMANENT/PROJ_INFO" "PERMANENT/PROJ_SRID"
[7] "PERMANENT/PROJ_UNITS" "PERMANENT/PROJ_WKT"
[9] "PERMANENT/WIND"
> execGRASS("g.gisenv")
GISDBASE='/tmp/Rtmpe7QdVd';
LOCATION_NAME='file28aaf5be4b905';
MAPSET='file28aaf6dc1c44c';
GRASS_GUI='text';
We may now write R objects to the temporary GRASS location for manipulation and analysis, here calculating slope and aspect layers:
> write_RAST(r, vname="terra_elev") Importing raster map <terra_elev>... 100% SpatRaster read into GRASS using r.in.gdal from file > execGRASS("g.list", type="raster", mapset=loc$MAPSET) terra_elev > execGRASS("r.slope.aspect", flags="overwrite", elevation="terra_elev", slope="slope", aspect="aspect") 100% Aspect raster map <aspect> complete Slope raster map <slope> complete > u1 <- read_RAST(c("terra_elev", "slope", "aspect")) Checking GDAL data type and nodata value... 100% Using GDAL data type <UInt16> Exporting raster data to RRASTER format... 100% r.out.gdal complete. File </tmp/RtmpLsAbI6/file29f4b33cd20f6.grd> created. Checking GDAL data type and nodata value... 100% Using GDAL data type <Float32> Exporting raster data to RRASTER format... 100% r.out.gdal complete. File </tmp/RtmpLsAbI6/file29f4b2d2e045b.grd> created. Checking GDAL data type and nodata value... 100% Using GDAL data type <Float32> Exporting raster data to RRASTER format... 100% r.out.gdal complete. File </tmp/RtmpLsAbI6/file29f4b52cab445.grd> created. > u1 class : SpatRaster dimensions : 90, 95, 3 (nrow, ncol, nlyr) resolution : 0.008333326, 0.008333333 (x, y) extent : 5.741667, 6.533333, 49.44167, 50.19167 (xmin, xmax, ymin, ymax) coord. ref. : lon/lat WGS 84 (EPSG:4326) sources : file29f4b33cd20f6.grd file29f4b2d2e045b.grd file29f4b52cab445.grd names : terra_elev, slope, aspect min values : 141.00000000, 0.01416342, 0.08974174 max values : 547.000000, 7.229438, 360.000000
Existing GRASS location
Similarly, GRASS may be started in an R session with an existing location by providing the gisDbase=, location= and mapset= arguments with valid values:
$ GRASS_INSTALLATION=/home/rsb/topics/grass/g832/grass83 R R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) ... > library(rgrass) GRASS GIS interface loaded with GRASS version: (GRASS not running) > GRASS_INSTALLATION <- Sys.getenv("GRASS_INSTALLATION") > loc <- initGRASS(GRASS_INSTALLATION, home=tempdir(), gisDbase="/home/rsb/topics/grassdata", location="nc_basic_spm_grass7", mapset="rsb", override=TRUE) > execGRASS("g.gisenv") GISDBASE='/home/rsb/topics/grassdata'; LOCATION_NAME='nc_basic_spm_grass7'; MAPSET='rsb'; GRASS_GUI='text'; > execGRASS("g.list", type="raster", mapset="PERMANENT") basins elevation elevation_shade geology lakes landuse soils
References
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