Difference between revisions of "R statistics/rgrass7"

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m (GRASS within R)
(finish updating to north carolina)
Line 291: Line 291:
 
</pre>
 
</pre>
  
'''To be updated'''
+
<pre>
 
+
library(rgrass7)
  # get path to GRASS binaries:
+
# initialisation and the use of north carolina dataset
  grass70 --config path
+
initGRASS(gisBase = "/home/veroandreo/software/grass-7.0.svn/dist.x86_64-unknown-linux-gnu",
 +
          home = tempdir(),
 +
          gisDbase = "/home/veroandreo/grassdata/",
 +
          location = "nc_spm_08_grass7", mapset = "user1", SG="elevation",
 +
          override = TRUE)
 +
# set region to default
 +
system("g.region -dp")
 +
# verify
 +
gmeta()
 +
# read data into R
 +
ncdata <- readRAST(c("geology_30m", "elevation"), cat=c(TRUE, FALSE))
 +
# summary of geology map
 +
summary(ncdata$geology_30m)
 +
proc.time()
 +
</pre>
  
 
The result is (shorted here):
 
The result is (shorted here):
Line 300: Line 314:
 
     cat batch.Rout
 
     cat batch.Rout
 
      
 
      
     R version 2.10.0 (2009-10-26)
+
     R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
     Copyright (C) 2009 The R Foundation for Statistical Computing
+
     Copyright (C) 2015 The R Foundation for Statistical Computing
     ISBN 3-900051-07-0
+
     Platform: x86_64-redhat-linux-gnu (64-bit)
 
     ...
 
     ...
 
     > library(rgrass7)
 
     > library(rgrass7)
 
     Loading required package: sp
 
     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
 
     Loading required package: XML
 
     GRASS GIS interface loaded with GRASS version: (GRASS not running)
 
     GRASS GIS interface loaded with GRASS version: (GRASS not running)
    >
+
     > # initialisation and the use of north carolina dataset
     > # initialisation and the use of spearfish60 data
+
     > initGRASS(gisBase = "/home/veroandreo/software/grass-7.0.svn/dist.x86_64-unknown-linux-gnu", home = tempdir(),  
     > initGRASS(gisBase = "/home/neteler/software/grass70/dist.x86_64-unknown-linux-gnu", home = tempdir(), gisDbase = "/home/neteler/grassdata/",
+
    +          gisDbase = "/home/veroandreo/grassdata/",
     +          location = "spearfish60", mapset = "user1", SG="elevation.dem", override = TRUE)
+
     +          location = "nc_spm_08_grass7", mapset = "user1", SG="elevation",
     gisdbase    /home/neteler/grassdata/  
+
    +          override = TRUE)
     location    spearfish60
+
     gisdbase    /home/veroandreo/grassdata/  
 +
     location    nc_spm_08_grass7
 
     mapset      user1  
 
     mapset      user1  
     rows        477
+
     rows        620
     columns    634
+
     columns    1630
     north      4928010
+
     north      320000
     south      4913700
+
     south      10000
     west        589980
+
     west        120000
     east        609000
+
     east        935000
     nsres      30
+
     nsres      500
     ewres      30
+
     ewres      500
     projection  +proj=utm +zone=13 +a=6378206.4 +rf=294.9786982 +no_defs
+
     projection  +proj=lcc +lat_1=36.16666666666666 +lat_2=34.33333333333334
     +nadgrids=/usr/local/grass-6.4.1/etc/nad/conus +to_meter=1.0  
+
    +lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
     Warning messages:
+
     +rf=298.257222101 +towgs84=0.000,0.000,0.000 +to_meter=1  
     1: In dir.create(gisDbase) : '/home/neteler/grassdata' already exists
+
   
     2: In dir.create(loc_path) :
+
    > system("g.region -dp")
       '/home/neteler/grassdata//spearfish60' already exists
+
    projection: 99 (Lambert Conformal Conic)
     >
+
    zone:      0
     > system("g.region -d")
+
     datum:     nad83
     > # verify
+
     ellipsoid: a=6378137 es=0.006694380022900787
     > gmeta6()
+
    north:     320000
     gisdbase    /home/neteler/grassdata/  
+
     south:     10000
     location    spearfish60
+
    west:       120000
 +
    east:       935000
 +
    nsres:      500
 +
    ewres:      500
 +
     rows:      620
 +
     cols:      1630
 +
     cells:      1010600
 +
     > gmeta()
 +
     gisdbase    /home/veroandreo/grassdata/  
 +
     location    nc_spm_08_grass7
 
     mapset      user1  
 
     mapset      user1  
     rows        477
+
     rows        620
     columns    634
+
     columns    1630
     north      4928010
+
     north      320000
 +
    south      10000
 +
    ...
 +
    > ncdata <- readRAST(c("geology_30m", "elevation"), cat=c(TRUE, FALSE))
 
     ...
 
     ...
    >
+
     > summary(ncdata$geology_30m)
    > spear <- readRAST6(c("geology", "elevation.dem"),
+
     CZfg_217 CZlg_262 CZig_270 CZbg_405 CZve_583 CZam_720 CZg_766 CZam_862
    +          cat=c(TRUE, FALSE), ignore.stderr=TRUE,
+
        292       78      277      102        8        1        2       25
    +          plugin=NULL)
+
     CZbg_910  Km_921 CZam_946    NA's  
    >
+
           18        5       2  1009790
     > summary(spear$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()
 
     > proc.time()
 
       user  system elapsed  
 
       user  system elapsed  
       2.891   0.492  3.412
+
       8.061   2.016  10.048
 +
 
  
 
[[Category:FAQ]]
 
[[Category:FAQ]]

Revision as of 15:58, 3 August 2015

This page refers to the usage of R within a GRASS GIS 7 session and the use of GRASS GIS 7 within an R session. (see also R_statistics/spgrass6)

R within GRASS

Startup

  • First start a GRASS GIS session. Then, at the GRASS command line start R (for a 'rstudio' session, see below)
In this example we will use the North Carolina sample dataset.

Reset the region settings to the defaults

GRASS 7.0.1svn (nc_spm_08_grass7):~ > g.region -d

Launch R from the GRASS prompt

GRASS 7.0.1svn (nc_spm_08_grass7):~ > R

Load the rgrass7 library:

> library(rgrass7)

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

> G <- gmeta()
gisdbase    /home/neteler/grassdata 
location    nc_spm_08_grass7 
mapset      user1 
rows        620 
columns     1630 
north       320000 
south       10000 
west        120000 
east        935000 
nsres       500 
ewres       500 
projection  +proj=lcc +lat_1=36.16666666666666 +lat_2=34.33333333333334
+lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
+rf=298.257222101 +towgs84=0.000,0.000,0.000 +to_meter=1 

Listing of existing maps

List available vector maps:

> execGRASS("g.list", parameters = list(type = "vector"))

List selected vector maps (wildcard):

> execGRASS("g.list", parameters = list(type = "vector", pattern = "precip*"))

Save selected vector maps into R vector:

> my_vmaps <- execGRASS("g.list", parameters = list(type = "vector", pattern = "precip*"))
> attributes(my_vmaps)
> attributes(my_vmaps)$resOut

List available raster maps:

> execGRASS("g.list", parameters = list(type = "raster"))

List selected raster maps (wildcard):

> execGRASS("g.list", parameters = list(type = "raster", pattern = "lsat7_2002*"))

Reading in data

Read in two raster maps (North Carolina sample dataset):

> ncdata <- readRAST(c("geology_30m", "elevation"), 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, in this case a SpatialGridDataFrame object filled with data from two North Carolina layers. Here is a plot of the elevation data:

> image(ncdata, attr = 2, col = terrain.colors(20))

Add a title to the plot:

> title("North Carolina elevation")
Ncdata.png

In addition, we can show what is going on inside the objects read into R:

> str(G)
List of 26
 $ DEBUG        : chr "0"
 $ LOCATION_NAME: chr "nc_spm_08_grass7"
 $ GISDBASE     : chr "/home/veroandreo/grassdata"
 $ MAPSET       : chr "PERMANENT"
 $ GUI          : chr "wxpython"
 $ projection   : chr "99"
 $ zone         : chr "0"
 $ n            : num 228500
 $ s            : num 215000
 $ w            : num 630000
 $ e            : num 645000
 $ t            : num 1
 $ b            : num 0
 $ nsres        : num 27.5
 $ nsres3       : num 10
 $ ewres        : num 37.5
 $ ewres3       : num 10
 $ tbres        : num 1
 $ rows         : int 491
 $ rows3        : int 1350
 $ cols         : int 400
 $ cols3        : int 1500
 $ depths       : int 1
 $ cells        : chr "196400"
 $ cells3       : chr "2025000"
 $ proj4        : chr "+proj=lcc +lat_1=36.16666666666666 +lat_2=34.33333333333334 +lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137 +"| __truncated__
 - attr(*, "class")= chr "gmeta"
> summary(ncdata)
Object of class SpatialGridDataFrame
Coordinates:
        min    max
[1,] 630000 645000
[2,] 215000 228500
Is projected: TRUE 
proj4string :
[+proj=lcc +lat_1=36.16666666666666 +lat_2=34.33333333333334
+lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
+rf=298.257222101 +towgs84=0.000,0.000,0.000 +to_meter=1]
Grid attributes:
  cellcentre.offset cellsize cells.dim
1          630018.8 37.50000       400
2          215013.7 27.49491       491
Data attributes:
   geology_30m      elevation     
 CZfg_217:70381   Min.   : 55.92  
 CZig_270:66861   1st Qu.: 94.78  
 CZbg_405:24561   Median :108.88  
 CZlg_262:19287   Mean   :110.38  
 CZam_862: 6017   3rd Qu.:126.78  
 CZbg_910: 4351   Max.   :156.25  
 (Other) : 4942                   

Summarizing data

We can create a table of cell counts:

> table(ncdata$geology_30m)
CZfg_217 CZlg_262 CZig_270 CZbg_405 CZve_583 CZam_720 CZg_766 CZam_862 CZbg_910 Km_921 CZbg_945 CZam_946 CZam_948
70381 19287 66861 24561 2089 467 691 6017 4351 1211 1 398 85

And compare with the equivalent GRASS module:

> execGRASS("r.stats", flags=c("c", "l"), parameters=list(input="geology_30m"), ignore.stderr=TRUE)
217 CZfg 70381
262 CZlg 19287
270 CZig 66861
405 CZbg 24561
583 CZve 2089
720 CZam 467
766 CZg 691
862 CZam 6017
910 CZbg 4351
921 Km 1211
945 CZbg 1
946 CZam 398
948 CZam 85

Create a box plot of geologic types at different elevations:

> boxplot(ncdata$elevation ~ ncdata$geology_30m, medlwd = 1)
Boxplot geo.png

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)

> ncdata$sqdem <- sqrt(ncdata$elevation)

Export data from R back into a GRASS raster map:

> writeRAST(ncdata, "sqdemNC", zcol="sqdem", ignore.stderr=TRUE)

Check that it imported into GRASS ok:

> execGRASS("r.info", parameters=list(map="sqdemNC"))
 +----------------------------------------------------------------------------+
 | Map:      sqdemNC                        Date: Sun Jul 19 13:06:34 2015    |
 | Mapset:   PERMANENT                      Login of Creator: veroandreo      |
 | Location: nc_spm_08_grass7                                                 |
 | DataBase: /home/veroandreo/grassdata                                       |
 | Title:     ( sqdemNC )                                                     |
 | Timestamp: none                                                            |
 |----------------------------------------------------------------------------|
 |                                                                            |
 |   Type of Map:  raster               Number of Categories: 0               |
 |   Data Type:    DCELL                                                      |
 |   Rows:         491                                                        |
 |   Columns:      400                                                        |
 |   Total Cells:  196400                                                     |
 |        Projection: Lambert Conformal Conic                                 |
 |            N:     228500    S: 215000.0002   Res: 27.49490794              |
 |            E:     645000    W:     630000   Res:  37.5                     |
 |   Range of data:    min = 7.47818253045085  max = 12.5000787351036         |
 |                                                                            |
 |   Data Description:                                                        |
 |    generated by r.in.bin                                                   |
 |                                                                            |
 |   Comments:                                                                |
 |                                                                            |
 +----------------------------------------------------------------------------+

Calling RStudio from a GRASS GIS session

If you are most used to run R through RStudio, but still want to have all GRASS data available for performing any analyses without loosing the possibility of still using GRASS command line, you can run:

GRASS> rstudio &

or, if you already are working on a certain RStudio project:

GRASS> rstudio /path/to/project/folder/ &

Then, you load rgrass7 library in your RStudio project

> library(rgrass7) 

and you are ready to go.


GRASS within R

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):

 grass70 --config path

It may report something like:

 /home/veroandreo/software/grass-7.0.svn/dist.x86_64-unknown-linux-gnu

To call GRASS GIS 7 functionality from R, start R and use the initGRASS() function to define the GRASS settings:

library(rgrass7)
    
# initialisation and the use of North Carolina sample dataset
initGRASS(gisBase = "/home/veroandreo/software/grass-7.0.svn/dist.x86_64-unknown-linux-gnu", home = tempdir(), 
          gisDbase = "/home/veroandreo/grassdata/",
          location = "nc_spm_08_grass7", mapset = "user1", SG="elevation",
          override = TRUE)

# set computational region to default (facultative)
system("g.region -dp")
# verify metadata
gmeta()

# get two raster maps into R space
ncdata <- readRAST(c("geology_30m", "elevation"), cat=c(TRUE, FALSE))

# calculate object summaries
summary(ncdata$geology_30m)
 CZfg_217 CZlg_262 CZig_270 CZbg_405 CZve_583 CZam_720  CZg_766 CZam_862 
     292       78      277      102        8        1        2       25 
 CZbg_910   Km_921 CZam_946     NA's 
      18        5        2  1009790 

R in GRASS in batch mode

Run the following script with

R CMD BATCH batch.R
library(rgrass7)
# initialisation and the use of north carolina dataset
initGRASS(gisBase = "/home/veroandreo/software/grass-7.0.svn/dist.x86_64-unknown-linux-gnu", 
          home = tempdir(), 
          gisDbase = "/home/veroandreo/grassdata/",
          location = "nc_spm_08_grass7", mapset = "user1", SG="elevation",
          override = TRUE)
# set region to default
system("g.region -dp")
# verify
gmeta()
# read data into R
ncdata <- readRAST(c("geology_30m", "elevation"), cat=c(TRUE, FALSE))
# summary of geology map
summary(ncdata$geology_30m)
proc.time()

The result is (shorted here):

   cat batch.Rout
   
   R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
   Copyright (C) 2015 The R Foundation for Statistical Computing
   Platform: x86_64-redhat-linux-gnu (64-bit)
   ...
   > library(rgrass7)
   Loading required package: sp
   Loading required package: XML
   GRASS GIS interface loaded with GRASS version: (GRASS not running)
   > # initialisation and the use of north carolina dataset
   > initGRASS(gisBase = "/home/veroandreo/software/grass-7.0.svn/dist.x86_64-unknown-linux-gnu", home = tempdir(), 
   +           gisDbase = "/home/veroandreo/grassdata/",
   +           location = "nc_spm_08_grass7", mapset = "user1", SG="elevation",
   +           override = TRUE)
   gisdbase    /home/veroandreo/grassdata/ 
   location    nc_spm_08_grass7 
   mapset      user1 
   rows        620 
   columns     1630 
   north       320000 
   south       10000 
   west        120000 
   east        935000 
   nsres       500 
   ewres       500 
   projection  +proj=lcc +lat_1=36.16666666666666 +lat_2=34.33333333333334
   +lat_0=33.75 +lon_0=-79 +x_0=609601.22 +y_0=0 +no_defs +a=6378137
   +rf=298.257222101 +towgs84=0.000,0.000,0.000 +to_meter=1 
   
   > system("g.region -dp")
   projection: 99 (Lambert Conformal Conic)
   zone:       0
   datum:      nad83
   ellipsoid:  a=6378137 es=0.006694380022900787
   north:      320000
   south:      10000
   west:       120000
   east:       935000
   nsres:      500
   ewres:      500
   rows:       620
   cols:       1630
   cells:      1010600
   > gmeta()
   gisdbase    /home/veroandreo/grassdata/ 
   location    nc_spm_08_grass7 
   mapset      user1 
   rows        620 
   columns     1630 
   north       320000 
   south       10000 
   ...
   > ncdata <- readRAST(c("geology_30m", "elevation"), cat=c(TRUE, FALSE))
   ...
   > summary(ncdata$geology_30m)
   CZfg_217 CZlg_262 CZig_270 CZbg_405 CZve_583 CZam_720  CZg_766 CZam_862 
        292       78      277      102        8        1        2       25 
   CZbg_910   Km_921 CZam_946     NA's 
         18        5        2  1009790 
   > proc.time()
      user  system elapsed 
     8.061   2.016  10.048