Veroandreo: /* GRASS within R */ more formatting

2016-09-15T18:02:32Z

GRASS within R: more formatting

← Older revision		Revision as of 18:02, 15 September 2016
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	To call GRASS GIS 6 functionality from R, use the initGRASS() function to define the GRASS settings:		To call GRASS GIS 6 functionality from R, use the initGRASS() function to define the GRASS settings:

	> library(spgrass6)		<source lang="rsplus">
			library(spgrass6)

	# initialisation and the use of spearfish60 data		# initialisation and the use of spearfish60 data
	> initGRASS(gisBase = "/usr/local/grass-6.4.1", home = tempdir(),		initGRASS(gisBase = "/usr/local/grass-6.4.1", home = tempdir(),
	gisDbase = "/home/neteler/grassdata/",		gisDbase = "/home/neteler/grassdata/",
	location = "spearfish60", mapset = "user1", SG="elevation.dem",		location = "spearfish60", mapset = "user1", SG="elevation.dem",
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	summary(spear$geology)		summary(spear$geology)
			</source>

	Run this script with		Run this script with

	R CMD BATCH batch.R		<source lang="bash">
			R CMD BATCH batch.R
			</source>

	The result is (shorted here):		The result is (shorted here):

	cat batch.Rout		<source lang="bash">
			cat batch.Rout
			</source>

			<source lang="rsplus">
	R version 2.10.0 (2009-10-26)		R version 2.10.0 (2009-10-26)
	Copyright (C) 2009 The R Foundation for Statistical Computing		Copyright (C) 2009 The R Foundation for Statistical Computing
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	user system elapsed		user system elapsed
	2.891 0.492 3.412		2.891 0.492 3.412
			</source>

	[[Category:FAQ]]		[[Category:FAQ]]

Veroandreo: /* R within GRASS */ more formatting

2016-09-15T17:59:34Z

R within GRASS: more formatting

Show changes

Veroandreo at 17:18, 19 July 2015

2015-07-19T17:18:20Z

← Older revision		Revision as of 17:18, 19 July 2015
Line 52:		Line 52:

	In addition, we can show what is going on inside the objects read into R:		In addition, we can show what is going on inside the objects read into R:
	> ~~'''~~str(G)~~'''~~		> str(G)
	<pre>		<pre>
	List of 26		List of 26

Veroandreo: add GRASS within R section

2015-07-19T17:16:38Z

add GRASS within R section

Show changes

Neteler at 14:29, 19 July 2015

2015-07-19T14:29:49Z

← Older revision		Revision as of 14:29, 19 July 2015
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	'''This page refers to the usage of R within a GRASS GIS 6 session.'''		'''This page refers to the usage of R within a GRASS GIS 6 session.''' (see also [[R_statistics/rgrass7]])

	=== Startup ===		=== Startup ===

Neteler: Moved here from R_statistics

2015-07-19T14:28:18Z

Moved here from R_statistics

New page

'''This page refers to the usage of R within a GRASS GIS 6 session.'''

=== Startup ===

* First start a GRASS session. Then, at the GRASS command line start ''R''.
: ''In this example we will use the sample Spearfish dataset.''

Reset the region settings to the defaults
GRASS> g.region -d

Launch R from the GRASS prompt
GRASS> R

Load the ''spgrass6'' library:
> library(spgrass6)

Get the GRASS environment (mapset, region, map projection, etc.); you can display the metadata for your location by printing G:
> G <- gmeta6()

=== Listing of existing maps ===

List available vector maps:
execGRASS("g.list", parameters = list(type = "vect"))

List selected vector maps (wildcard):
execGRASS("g.list", parameters = list(type = "vect", pattern = "precip*"))

Save selected vector maps into R vector:
my_vmaps <- execGRASS("g.list", parameters = list(type = "vect", pattern = "precip*"))
attributes(my_vmaps)
attributes(my_vmaps)$resOut

List available raster maps:
execGRASS("g.list", parameters = list(type = "rast"))

List selected raster maps (wildcard):
execGRASS("g.list", parameters = list(type = "rast", pattern = "lsat7_2000*"))

=== Reading in data ===
Read in two raster maps (Spearfish sample dataset):
> spear <- readRAST6(c("geology", "elevation.dem"),
cat=c(TRUE, FALSE), ignore.stderr=TRUE,
plugin=NULL)

The metadata are accessed and available, but are not (yet) used to structure the ''sp'' class objects, here a SpatialGridDataFrame object filled with data from two Spearfish layers. Here is a plot of the elevation data:
> image(spear, attr = 2, col = terrain.colors(20))

Add a title to the plot:
> title("Spearfish elevation")

[[Image:R_stats_elev.png|center]]

In addition, we can show what is going on inside the objects read into R:
> '''str(G)'''
<pre>
List of 26
$ GISDBASE : chr "/home/rsb/topics/grassdata"
$ LOCATION_NAME: chr "spearfish57"
$ MAPSET : chr "rsb"
$ DEBUG : chr "0"
$ GRASS_GUI : chr "text"
$ projection : chr "1 (UTM)"
$ zone : chr "13"
$ datum : chr "nad27"
$ ellipsoid : chr "clark66"
$ north : num 4928010
$ south : num 4913700
$ west : num 589980
$ east : num 609000
$ top : num 1
$ bottom : num 0
$ nsres : num 30
$ nsres3 : num 30
$ ewres : num 30
$ ewres3 : num 30
$ tbres : num 1
$ rows : int 477
$ rows3 : int 477
$ cols : int 634
$ cols3 : int 634
$ depths : int 1
$ proj4 : chr "+proj=utm +zone=13 +a=6378206.4 +rf=294.9786982 +no_defs +nadgrids=/home/rsb/topics/grass61/grass-6.1.cvs/etc/nad/conus"
</pre>

> '''summary(spear)'''
<pre>
Object of class SpatialGridDataFrame
Coordinates:
min max
coords.x1 589980 609000
coords.x2 4913700 4928010
Is projected: TRUE
proj4string : [+proj=utm +zone=13 +a=6378206.4 +rf=294.9786982 +no_defs +nadgrids=/home/rsb/topics/grass61/grass-6.1.cvs/etc/nad/conus]
Number of points: 2
Grid attributes:
cellcentre.offset cellsize cells.dim
1 589995 30 634
2 4913715 30 477
Data attributes:
geology elevation.dem
sandstone:74959 Min. : 1066
limestone:61355 1st Qu.: 1200
shale :46423 Median : 1316
sand :36561 Mean : 1354
igneous :36534 3rd Qu.: 1488
(Other) :37636 Max. : 1840
NA's : 8950 NA's :10101
</pre>

=== Summarizing data ===

We can create a table of cell counts:
> '''table(spear$geology)'''
{| class="wikitable" border="1"
!metamorphic
!transition
!igneous
!sandstone
!limestone
!shale
!sandy shale
!claysand
!sand
|-
|11693
|142
|36534
|74959
|61355
|46423
|11266
|14535
|36561
|}

And compare with the equivalent GRASS module:
> '''execGRASS("r.stats", flags=c("c", "l"), parameters=list(input="geology"), ignore.stderr=TRUE)'''
<pre>
1 metamorphic 11693
2 transition 142
3 igneous 36534
4 sandstone 74959
5 limestone 61355
6 shale 46423
7 sandy shale 11266
8 claysand 14535
9 sand 36561
* no data 8950
</pre>

Create a box plot of geologic types at different elevations:
> '''boxplot(spear$elevation.dem ~ spear$geology, medlwd = 1)'''

[[Image:R_stats_boxplot_geo.png|center]]

=== Exporting data back to GRASS ===

Finally, a SpatialGridDataFrame object is written back to a GRASS raster map:

First prepare some data: (square root of elevation)
> spear$sqdem <- sqrt(spear$elevation.dem)

Export data from ''R'' back into a GRASS raster map:
> writeRAST6(spear, "sqdemSP", zcol="sqdem", ignore.stderr=TRUE)

Check that it imported into GRASS ok:
> '''execGRASS("r.info", parameters=list(map="sqdemSP"))'''

<pre>
+----------------------------------------------------------------------------+
| Layer: sqdemSP Date: Sun May 14 21:59:26 2006 |
| Mapset: rsb Login of Creator: rsb |
| Location: spearfish57 |
| DataBase: /home/rsb/topics/grassdata |
| Title: ( sqdemSP ) |
|----------------------------------------------------------------------------|
| |
| Type of Map: raster Number of Categories: 255 |
| Data Type: FCELL |
| Rows: 477 |
| Columns: 634 |
| Total Cells: 302418 |
| Projection: UTM (zone 13) |
| N: 4928010 S: 4913700 Res: 30 |
| E: 609000 W: 589980 Res: 30 |
| Range of data: min = 32.649654 max = 42.895222 |
| |
| Data Source: |
| |
| |
| |
| Data Description: |
| generated by r.in.gdal |
| |
| |
+----------------------------------------------------------------------------+
</pre>

=== v.krige usage example ===

v.krige is a GRASS python script (Addon) which performs kriging operations in the GRASS environment, using R functions for the back-end interpolation. It is present in GRASS 6.5svn, and further developed in GRASS 7svn. It requires a number of dependencies: '''python-rpy2''' (''needs to be "Rpy2", "Rpy" will not do'' unless it is rpy 2.x), then the following R-CRAN packages:
* gstat, spgrass6 (as above)
install.packages(c("gstat","spgrass6"))
* maptools
install.packages("maptools")
* automap (optional), with gpclib (or rgeos)
install.packages("automap")
install.packages("rgeos")

[[Category:FAQ]]
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[[Category:R]]
[[Category:Statistics]]

R statistics/spgrass6 - Revision history

Veroandreo: /* GRASS within R */ more formatting

Veroandreo: /* R within GRASS */ more formatting

Veroandreo at 17:18, 19 July 2015

Veroandreo: add GRASS within R section

Neteler at 14:29, 19 July 2015

Neteler: Moved here from R_statistics