R statistics/rgrass - Revision history

Veroandreo: /* GRASS within R */

2023-04-21T19:48:29Z

GRASS within R

← Older revision		Revision as of 19:48, 21 April 2023
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	The first argument in initGRASS() is gisBase=. This argument refers to the path where GRASS is installed. In the latest rgrass		The first argument in initGRASS() is gisBase=. This argument refers to the path where GRASS is installed. In the latest rgrass
	version, 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 <tt>grass --config path</> will be tried to get the value of GISBASE that corresponds to the GRASS installation in the system PATH (if any).		version, 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 <tt>grass --config path</tt> will be tried to get the value of GISBASE that corresponds to the GRASS installation in the system PATH (if any).

	If users, still want/need to pass the path to GRASS installation themselves, they can run:		If users, still want/need to pass the path to GRASS installation themselves, they can run:

Veroandreo at 19:47, 21 April 2023

2023-04-21T19:47:54Z

← Older revision		Revision as of 19:47, 21 April 2023
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	override = TRUE)		override = TRUE)
	</source>		</source>


	=== Temporary location ===		=== Temporary location ===

Veroandreo: /* Example 1: raster maps */

2023-04-21T19:41:06Z

Example 1: raster maps

← Older revision		Revision as of 19:41, 21 April 2023
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	==== Example 1: raster maps ====		==== Example 1: raster maps ====

	~~Manual page: [https://search.r-project.org/CRAN/refmans/rgrass/html/readRAST.html read_RAST()]~~

	Read two GRASS raster maps, "geology_30m" and "elevation", from the North Carolina sample data location into the R current session as a new object "ncdata". This object is a SpatRaster layer from terra package:		Read two GRASS raster maps, "geology_30m" and "elevation", from the North Carolina sample data location into the R current session as a new object "ncdata". This object is a SpatRaster layer from terra package:
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	</source>		</source>

	[[Image:~~ncdata~~.png\|center]]		[[Image:ncdata_new.png\|center]]

	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:

Veroandreo: edit batch section

2023-04-21T19:39:24Z

edit batch section

Show changes

Veroandreo: GRASS in R - rewrite most of the section

2023-04-21T19:10:03Z

GRASS in R - rewrite most of the section

← Older revision		Revision as of 19:10, 21 April 2023
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	== GRASS within R ==		== GRASS within R ==

	~~Using '''~~GRASS ~~GIS~~ within a R ~~session''', i.e. you connect to a GRASS GIS location/mapset from within R (or RStudio).~~		== GRASS within R ==

	~~=== Startup ===~~		In this case, we start '''GRASS GIS within an R session''', i.e., we use <tt>initGRASS()</tt> to start GRASS in a temporary location or in an existing GRASS GIS location.

	In the ~~first place~~, ~~find out~~ the path to the GRASS ~~GIS library. This can be easily done with~~ the ~~following command (still outside of R; or through a~~ system() ~~call inside of R)~~:		The first argument in initGRASS() is gisBase=. This argument refers to the path where GRASS is installed. In the latest rgrass
			version, 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 <tt>grass --config path</> will be tried to get the value of GISBASE that corresponds to the GRASS installation in the system PATH (if any).

			If users, in any case want to pass the path to GRASS installation themselves, they can run:

	<source lang="bash">		<source lang="bash">
	# OSGeo4W, Linux, Mac OSX users:		# OSGeo4W shell, Linux, Mac OSX users:
	grass --config path		grass --config path
	</source>		</source>
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	</source>		</source>

	~~To call GRASS GIS functionality from R, start R and use the initGRASS() function to define the GRASS settings.~~ If GRASS GIS was		If GRASS GIS was installed through OSGeo4W, users should first start the OSGeo4W Shell. Note that it may start in C: or a directory
	installed through OSGeo4W, first start the OSGeo4W Shell. Note that it may start in C: or a directory where the user does not have		where the user does not have writing permission. Before calling R or RStudio, first change to a directory where you are
	writing permission. Before calling R or RStudio, first change to a directory where you are sure you have writing permission.		sure you have writing permission.

	<source lang="rsplus">		<source lang="rsplus">
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	gisDbase = "C:/Users/marissa/grassdata/",		gisDbase = "C:/Users/marissa/grassdata/",
	location = "nc_spm_08_grass7",		location = "nc_spm_08_grass7",
	mapset = "user1",		mapset = "user1",
	SG=~~"elevation"~~)		home=tempdir(),
			override = TRUE)
	</source>		</source>

	Linux and Mac OSX users just need to start R or RStudio the usual way, load the rgrass package and initialize GRASS ~~GIS with initGRASS()~~ as shown below:		Linux and Mac OSX users just need to start R or RStudio the usual way, load the rgrass package and initialize GRASS as shown below:

	<source lang="rsplus">		<source lang="rsplus">
	~~# load rgrass package~~
	library(rgrass)		library(rgrass)

	# initialisation of GRASS in the North Carolina sample dataset		# initialisation of GRASS in the North Carolina sample dataset
	initGRASS(gisBase = "/usr/~~local~~/~~grass~~",		initGRASS(gisBase = "/usr/lib64/grass82",
	~~home = tempdir()~~,
	gisDbase = "/home/veroandreo/grassdata/",		gisDbase = "/home/veroandreo/grassdata/",
	location = "~~nc_spm_08_grass7~~",		location = "nc_basic_spm_grass7",
	mapset = "user1",		mapset = "user1",
	SG=~~"elevation"~~)		home=tempdir(),
			override = TRUE)
	</source>		</source>

	~~Note: the optional SG parameter is~~ a ~~'SpatialGrid' object to~~ define ~~the ‘DEFAULT_WIND’ of~~ the temporary location.
			=== Temporary location ===

			If we don’t pass an existing location to initGRASS(), a temporary GRASS location will be created and set. By default this will be
			an XY location, i.e., no CRS defined. To define a CRS for the temporary location, we create a terra SpatRaster object that by default will be EPSG:4326.

	<source lang="rsplus">		<source lang="rsplus">
	~~# set computational region to default~~ (~~optional~~)		x <- rast()
	~~system~~(~~"g.region -dp"~~)		x
	~~# verify metadata~~		class : SpatRaster
	~~gmeta~~()		dimensions : 180, 360, 1 (nrow, ncol, nlyr)
			resolution : 1, 1 (x, y)
			extent : -180, 180, -90, 90 (xmin, xmax, ymin, ymax)
			coord. ref. : lon/lat WGS 84
			</source>

	~~# get two raster maps into R space~~		Then, we use that object to provide an EPSG to our temporary location via the SG= parameter and start GRASS:
	~~ncdata <- read_RAST(c("geology_30m"~~, ~~"elevation"), cat~~=~~c(TRUE, FALSE))~~

	~~# calculate object summaries~~		<source lang="rsplus">
	~~summary~~(~~ncdata$geology_30m~~)		initGRASS(home = tempdir(),
	~~CZfg_217 CZlg_262 CZig_270 CZbg_405 CZve_583 CZam_720 CZg_766 CZam_862~~		SG = x,
	~~292 78 277 102 8 1 2 25~~		override = TRUE)
	~~CZbg_910 Km_921 CZam_946 NA's~~
	~~18 5 2 1009790~~
	</source>		</source>

			After that, users can write raster and vector maps into GRASS with write_RAST() and write_VECT(), use GRASS GIS modules over those data with execGRASS() and export the results back to R with read_RAST() and read_VECT() as exemplified above.

			=== Existing location ===

			In the case of existing locations, users will provide the path to them as shown before and read data from GRASS database into R
			through read_RAST() and read_VECT(), do their analyses or modeling in R and potentially write results back into GRASS with write_RAST() and write_VECT().

	== R in GRASS in batch mode ==		== R in GRASS in batch mode ==

Veroandreo: /* Exporting data back to GRASS */ update exaple 5

2023-04-21T15:16:14Z

Exporting data back to GRASS: update exaple 5

← Older revision		Revision as of 15:16, 21 April 2023
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	Export data from ''R'' back into a GRASS raster map:		Export data from ''R'' back into a GRASS raster map:
	<source lang="rsplus">		<source lang="rsplus">
	~~writeRAST~~(ncdata, "sqdemNC", ~~zcol~~="~~sqdem~~", ~~ignore.stderr=TRUE~~)		write_RAST(ncdata$sqdem, "sqdemNC", flags = c("o","overwrite"))
	</source>		</source>

	Check that it imported ~~into GRASS ok~~:		Check that it imported properly:
	<source lang="rsplus">		<source lang="rsplus">
	execGRASS("r.info", parameters=list(map="sqdemNC"))		execGRASS("r.info", parameters=list(map="sqdemNC"))
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	<pre>		<pre>
	+----------------------------------------------------------------------------+		+----------------------------------------------------------------------------+
	\| Map: sqdemNC Date: ~~Sun Jul 19 13~~:06:~~34 2015~~ \|		\| Map: sqdemNC Date: Fri Apr 21 17:14:05 2023 \|
	\| Mapset: PERMANENT Login of Creator: veroandreo \|		\| Mapset: PERMANENT Login of Creator: veroandreo \|
	\| Location: nc_spm_08_grass7 \|		\| Location: nc_spm_08_grass7 \|
	\| DataBase: /home/veroandreo/grassdata \|		\| DataBase: /home/veroandreo/grassdata \|
	\| Title: ~~( sqdemNC )~~ \|		\| Title: \|
	\| Timestamp: none \|		\| Timestamp: none \|
	\|----------------------------------------------------------------------------\|		\|----------------------------------------------------------------------------\|
	\| \|		\| \|
	\| Type of Map: raster Number of Categories: 0 \|		\| Type of Map: raster Number of Categories: 0 \|
	\| Data Type: ~~DCELL~~ \|		\| Data Type: FCELL Semantic label: (none) \|
	\| Rows: ~~491~~ \|		\| Rows: 450 \|
	\| Columns: ~~400~~ \|		\| Columns: 500 \|
	\| Total Cells: ~~196400~~ \|		\| Total Cells: 225000 \|
	\| Projection: Lambert Conformal Conic \|		\| Projection: Lambert Conformal Conic \|
	\| N: 228500 S: 215000~~.0002~~ Res: ~~27.49490794~~ \|		\| N: 228500 S: 215000 Res: 30 \|
	\| E: 645000 W: 630000 Res: ~~37.5~~ \|		\| E: 645000 W: 630000 Res: 30 \|
	\| Range of data: min = 7.~~47818253045085~~ max = 12.~~5000787351036~~ \|		\| Range of data: min = 7.478182 max = 12.50008 \|
	\| \|		\| \|
	\| Data Description: \|		\| Data Description: \|
	\| generated by r.in.~~bin~~ \|		\| generated by r.in.gdal \|
	\| \|		\| \|
	\| Comments: \|		\| Comments: \|
			\| r.in.gdal --overwrite -o input="/home/veroandreo/tmp/grass8-veroandr\ \|
			\| eo-120898/RtmpPcRHkF/file1da12dbc5b5d.grd" output="sqdemNC" memory=3\ \|
			\| 00 offset=0 num_digits=0 \|
	\| \|		\| \|
	+----------------------------------------------------------------------------+		+----------------------------------------------------------------------------+

Veroandreo: /* Example 5: Querying maps */ edit example level

2023-04-21T15:05:33Z

Example 5: Querying maps: edit example level

← Older revision		Revision as of 15:05, 21 April 2023
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	--->		--->

	=== Example 5: Querying maps ===		==== Example 5: Querying maps ====

	Sometimes you may want to query GRASS GIS maps from your R session.		Sometimes you may want to query GRASS GIS maps from your R session. As an example, here the transfer of raster pixel values at the position of vector points:

	As an example, here the transfer of raster pixel values at the position of vector points:

	<source lang="rsplus">		<source lang="rsplus">
	# set the computational region ~~first~~ to the raster map:		# set the computational region to the raster map:
	execGRASS("g.region", raster = "elev_state_500m", flags = "p")		execGRASS("g.region", raster = "elev_state_500m", flags = "p")

Veroandreo: /* Example 4: Summarizing data */ remove boxplot, does not work with terra objects

2023-04-21T15:02:26Z

Example 4: Summarizing data: remove boxplot, does not work with terra objects

← Older revision		Revision as of 15:02, 21 April 2023
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	</source>		</source>

	=== Example 4: Summarizing data ===		==== Example 4: Summarizing data ====

	We can create a table of cell counts:		We can create a table of cell counts:
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	</pre>		</pre>

			<!--- it does no work with terra
	Create a box plot of geologic types at different elevations:		Create a box plot of geologic types at different elevations:
	<source lang="rsplus">		<source lang="rsplus">
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	[[Image:boxplot_geo.png\|center]]		[[Image:boxplot_geo.png\|center]]
			--->

	=== Example 5: Querying maps ===		=== Example 5: Querying maps ===

Veroandreo: /* Example 4: Summarizing data */ re-adding summary, it works just fine

2023-04-21T13:18:40Z

Example 4: Summarizing data: re-adding summary, it works just fine

← Older revision		Revision as of 13:18, 21 April 2023
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	=== Example 4: Summarizing data ===		=== Example 4: Summarizing data ===

	~~<!--- this does not coincide now using the function freq in terra, so removing~~
	We can create a table of cell counts:		We can create a table of cell counts:
	<source lang="rsplus">		<source lang="rsplus">
	~~table~~(ncdata$geology_30m)		freq(ncdata$geology_30m)
	</source>		</source>
	~~{\| class="wikitable" border="1"~~		<pre>
	~~!CZfg_217~~		layer value count
	~~!CZlg_262~~		1 1 217 80618
	~~!CZig_270~~		2 1 262 22076
	~~!CZbg_405~~		3 1 270 76597
	~~!CZve_583~~		4 1 405 28190
	~~!CZam_720~~		5 1 583 2401
	~~!CZg_766~~		6 1 720 536
	~~!CZam_862~~		7 1 766 786
	~~!CZbg_910~~		8 1 862 6858
	~~!Km_921~~		9 1 910 4996
	~~!CZbg_945~~		10 1 921 1392
	~~!CZam_946~~		11 1 945 1
	~~!CZam_948~~		12 1 946 452
	\|-		13 1 948 97
	~~\|70381~~		</pre>
	~~\|19287~~
	~~\|66861~~
	~~\|24561~~
	~~\|2089~~
	~~\|467~~
	~~\|691~~
	~~\|6017~~
	~~\|4351~~
	~~\|1211~~
	\|1
	~~\|398~~
	~~\|85~~
	\|}

	And compare with the equivalent GRASS module:		And compare with the equivalent GRASS module:
Line 247:		Line 233:
	</source>		</source>
	<pre>		<pre>
	217 CZfg ~~70381~~		217 CZfg 80618
	262 CZlg ~~19287~~		262 CZlg 22076
	270 CZig ~~66861~~		270 CZig 76597
	405 CZbg ~~24561~~		405 CZbg 28190
	583 CZve ~~2089~~		583 CZve 2401
	720 CZam ~~467~~		720 CZam 536
	766 CZg ~~691~~		766 CZg 786
	862 CZam ~~6017~~		862 CZam 6858
	910 CZbg ~~4351~~		910 CZbg 4996
	921 Km ~~1211~~		921 Km 1392
	945 CZbg 1		945 CZbg 1
	946 CZam ~~398~~		946 CZam 452
	948 CZam 85		948 CZam 97
	</pre>		</pre>
	~~--->~~

	Create a box plot of geologic types at different elevations:		Create a box plot of geologic types at different elevations:

Veroandreo: /* Reading in data from GRASS */ remove terra:: and call the library instead

2023-04-21T12:53:06Z

Reading in data from GRASS: remove terra:: and call the library instead

← Older revision		Revision as of 12:53, 21 April 2023
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	</source>		</source>

	=== Reading in data from GRASS ===		=== Reading data from GRASS ===

	==== Example 1: raster maps ====		==== Example 1: raster maps ====
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	==== Example 2: single raster map ====		==== Example 2: single raster map ====

	Here an example ~~for~~ a single raster map ~~transfer~~ from GRASS GIS to R:		Here an example to transfer a single raster map from GRASS GIS to R:

	<source lang="rsplus">		<source lang="rsplus">
	library(rgrass)		library(rgrass)
			library(terra)
	execGRASS("g.region", raster = "elevation", flags = "p")		execGRASS("g.region", raster = "elevation", flags = "p")
	ncdata <- read_RAST("elevation")		ncdata <- read_RAST("elevation")
	~~terra::~~summary(ncdata)		summary(ncdata)
	~~terra::~~plot(ncdata)		plot(ncdata)
	</source>		</source>

	==== Example 3: vector maps ====		==== Example 3: vector maps ====

	Here an example ~~for~~ a single vector map ~~transfer~~ from GRASS GIS to R. In this case, vector maps from GRASS will be converted into SpatVector objects from the terra package in R:		Here an example to transfer a single vector map from GRASS GIS to R. In this case, vector maps from GRASS will be converted into SpatVector objects from the terra package in R:

	<source lang="rsplus">		<source lang="rsplus">
	# needed prerequisite		# needed prerequisite
	library(rgrass)		library(rgrass)
			library(terra)
	execGRASS("v.info", map="schools_wake", layer="1")		execGRASS("v.info", map="schools_wake", layer="1")
	vInfo("schools_wake")		vInfo("schools_wake")
	myschools <- read_VECT("schools_wake")		myschools <- read_VECT("schools_wake")
	print(~~terra::~~summary(myschools))		print(summary(myschools))
	~~terra::~~plot(myschools)		plot(myschools)
	</source>		</source>

← Older revision		Revision as of 15:16, 21 April 2023
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	Export data from ''R'' back into a GRASS raster map:		Export data from ''R'' back into a GRASS raster map:
	<source lang="rsplus">		<source lang="rsplus">
	~~writeRAST~~(ncdata, "sqdemNC", ~~zcol~~="~~sqdem~~", ~~ignore.stderr=TRUE~~)		write_RAST(ncdata$sqdem, "sqdemNC", flags = c("o","overwrite"))
	</source>		</source>

	Check that it imported ~~into GRASS ok~~:		Check that it imported properly:
	<source lang="rsplus">		<source lang="rsplus">
	execGRASS("r.info", parameters=list(map="sqdemNC"))		execGRASS("r.info", parameters=list(map="sqdemNC"))
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	<pre>		<pre>
	+----------------------------------------------------------------------------+		+----------------------------------------------------------------------------+
	\| Map: sqdemNC Date: ~~Sun Jul 19 13~~:06:~~34 2015~~ \|		\| Map: sqdemNC Date: Fri Apr 21 17:14:05 2023 \|
	\| Mapset: PERMANENT Login of Creator: veroandreo \|		\| Mapset: PERMANENT Login of Creator: veroandreo \|
	\| Location: nc_spm_08_grass7 \|		\| Location: nc_spm_08_grass7 \|
	\| DataBase: /home/veroandreo/grassdata \|		\| DataBase: /home/veroandreo/grassdata \|
	\| Title: ~~( sqdemNC )~~ \|		\| Title: \|
	\| Timestamp: none \|		\| Timestamp: none \|
	\|----------------------------------------------------------------------------\|		\|----------------------------------------------------------------------------\|
	\| \|		\| \|
	\| Type of Map: raster Number of Categories: 0 \|		\| Type of Map: raster Number of Categories: 0 \|
	\| Data Type: ~~DCELL~~ \|		\| Data Type: FCELL Semantic label: (none) \|
	\| Rows: ~~491~~ \|		\| Rows: 450 \|
	\| Columns: ~~400~~ \|		\| Columns: 500 \|
	\| Total Cells: ~~196400~~ \|		\| Total Cells: 225000 \|
	\| Projection: Lambert Conformal Conic \|		\| Projection: Lambert Conformal Conic \|
	\| N: 228500 S: 215000~~.0002~~ Res: ~~27.49490794~~ \|		\| N: 228500 S: 215000 Res: 30 \|
	\| E: 645000 W: 630000 Res: ~~37.5~~ \|		\| E: 645000 W: 630000 Res: 30 \|
	\| Range of data: min = 7.~~47818253045085~~ max = 12.~~5000787351036~~ \|		\| Range of data: min = 7.478182 max = 12.50008 \|
	\| \|		\| \|
	\| Data Description: \|		\| Data Description: \|
	\| generated by r.in.~~bin~~ \|		\| generated by r.in.gdal \|
	\| \|		\| \|
	\| Comments: \|		\| Comments: \|
			\| r.in.gdal --overwrite -o input="/home/veroandreo/tmp/grass8-veroandr\ \|
			\| eo-120898/RtmpPcRHkF/file1da12dbc5b5d.grd" output="sqdemNC" memory=3\ \|
			\| 00 offset=0 num_digits=0 \|
	\| \|		\| \|
	+----------------------------------------------------------------------------+		+----------------------------------------------------------------------------+