rgrass-deprecated: Interface between GRASS geographical information system and R
In rgrass7: Deprecated Interface Between GRASS Geographical Information System and R
rgrass7-deprecated R Documentation
Interface between GRASS geographical information system and R
Description
Deprecated interpreted interface between GRASS geographical
information system, versions 7 and 8, and R, use rgrass instead.
Usage
execGRASS(cmd, flags = NULL, ..., parameters = NULL, intern = NULL,
ignore.stderr = NULL, Sys_ignore.stdout=FALSE, Sys_wait=TRUE,
Sys_input=NULL, Sys_show.output.on.console=TRUE, Sys_minimized=FALSE,
Sys_invisible=TRUE, echoCmd=NULL, redirect=FALSE, legacyExec=NULL)
stringexecGRASS(string, intern = NULL,
ignore.stderr = NULL, Sys_ignore.stdout=FALSE, Sys_wait=TRUE,
Sys_input=NULL, Sys_show.output.on.console=TRUE, Sys_minimized=FALSE,
Sys_invisible=TRUE, echoCmd=NULL, redirect=FALSE, legacyExec=NULL)
doGRASS(cmd, flags = NULL, ..., parameters = NULL, echoCmd=NULL,
legacyExec=NULL)
parseGRASS(cmd, legacyExec=NULL)
## S3 method for class 'GRASS_interface_desc'
print(x, ...)
getXMLencoding()
setXMLencoding(enc)
use_sf()
use_sp()
gmeta(ignore.stderr = FALSE, g.proj_WKT=NULL)
getLocationProj(ignore.stderr = FALSE, g.proj_WKT=NULL)
gmeta2grd(ignore.stderr = FALSE)
## S3 method for class 'gmeta'
print(x, ...)
get.ignore.stderrOption()
get.stop_on_no_flags_parasOption()
get.useGDALOption()
get.pluginOption()
get.echoCmdOption()
get.useInternOption()
get.legacyExecOption()
get.defaultFlagsOption()
get.suppressEchoCmdInFuncOption()
set.ignore.stderrOption(value)
set.stop_on_no_flags_parasOption(value)
set.useGDALOption(value)
set.pluginOption(value)
set.echoCmdOption(value)
set.useInternOption(value)
set.legacyExecOption(value)
set.defaultFlagsOption(value)
set.suppressEchoCmdInFuncOption(value)
initGRASS(gisBase, home, SG, gisDbase, addon_base, location, mapset,
override = FALSE, use_g.dirseps.exe = TRUE, pid, remove_GISRC=FALSE,
ignore.stderr=get.ignore.stderrOption())
get.GIS_LOCK()
set.GIS_LOCK(pid)
unset.GIS_LOCK()
unlink_.gislock()
remove_GISRC()
readRAST(vname, cat=NULL, ignore.stderr = get.ignore.stderrOption(),
NODATA=NULL, plugin=get.pluginOption(), mapset=NULL,
useGDAL=get.useGDALOption(), close_OK=TRUE, drivername="GTiff",
driverFileExt=NULL, return_SGDF=TRUE)
read_RAST(vname, cat=NULL, NODATA=NULL, ignore.stderr=get.ignore.stderrOption(),
return_format="SGDF", close_OK=return_format=="SGDF", flags=NULL)
writeRAST(x, vname, zcol = 1, NODATA=NULL,
ignore.stderr = get.ignore.stderrOption(), useGDAL=get.useGDALOption(),
overwrite=FALSE, flags=NULL, drivername="GTiff")
write_RAST(x, vname, zcol = 1, NODATA=NULL, flags=NULL,
ignore.stderr = get.ignore.stderrOption(), overwrite=FALSE, verbose=TRUE)
readVECT(vname, layer, type=NULL, plugin=NULL,
remove.duplicates = TRUE, ignore.stderr=NULL,
with_prj=TRUE, with_c=FALSE, mapset=NULL,
pointDropZ=FALSE, driver=NULL)
read_VECT(vname, layer, type=NULL, flags="overwrite",
ignore.stderr = NULL)
writeVECT(SDF, vname, v.in.ogr_flags=NULL,
ignore.stderr = NULL, driver=NULL,
min_area=0.0001, snap=-1)
write_VECT(x, vname, flags="overwrite", ignore.stderr = NULL)
vInfo(vname, layer, ignore.stderr = NULL)
vColumns(vname, layer, ignore.stderr = NULL)
vDataCount(vname, layer, ignore.stderr = NULL)
vect2neigh(vname, ID=NULL, ignore.stderr = NULL, remove=TRUE, vname2=NULL,
units="k")
Arguments
cmd
GRASS command name
flags
character vector of GRASS command flags
...
for execGRASS and doGRASS, GRASS module parameters given as R named arguments directly. For the print method, other arguments to print method. The storage modes of values passed must match thos required in GRASS, so a single GRASS string must be a character vector of length 1, a single GRASS integer must be an integer vector of length 1 (may be an integer constant such as 10L), and a single GRASS float must be a numeric vector of length 1. For multiple values, use vectors of suitable length
parameters
list of GRASS command parameters, used if GRASS parameters are not given as R arguments directly; the two methods for passing GRASS parameters may not be mixed. The storage modes of values passed must match thos required in GRASS, so a single GRASS string must be a character vector of length 1, a single GRASS integer must be an integer vector of length 1 (may be an integer constant such as 10L), and a single GRASS float must be a numeric vector of length 1. For multiple values, use vectors of suitable length
string
a string representing one full GRASS statement, using shell syntax: command name, optionally followed by flags and parameters, all separated by whitespaces.
Parameters follow the key=value format; if 'value' contains spaces, then 'value' must be quoted
intern
default NULL, in which case set internally from get.useInternOption; a logical (not 'NA') which indicates whether to make the output of the command an R object. Not available unless 'popen' is supported on the platform
ignore.stderr
default NULL, taking the value set by set.ignore.stderrOption, a logical indicating whether error messages written to 'stderr' should be ignored
Sys_ignore.stdout, Sys_wait, Sys_input
pass extra arguments to system
Sys_show.output.on.console, Sys_minimized, Sys_invisible
pass extra arguments to system on Windows systems only
echoCmd
default NULL, taking the logical value set by set.echoCmdOption, print GRASS command to be executed to console
redirect
default FALSE, if TRUE, add “2>&1” to the command string and set intern to TRUE; only used in legacy mode
legacyExec
default NULL, taking the logical value set by set.legacyExecOption which is initialised to FALSE on “unix” platforms and TRUE otherwise. If TRUE, use system, if FALSE use system2 and divert stderr to temporary file to record error messages and warnings from GRASS modules
x
object
enc
character string to replace UTF-8 in header of XML data generated by GRASS module –interface-description output when the internationalised messages are not in UTF-8 (known to apply to French, which is in latin1)
g.proj_WKT
default NULL: return WKT2 representation in GRASS >= 7.6 and Proj4 in GRASS < 7.6; may be set to FALSE to return Proj4 for GRASS >= 7.6
value
logical value for setting options on ignore.stderr set by default on package load to FALSE, stop_on_no_flags_paras set by default on package load to TRUE, useGDAL set by default on package load to TRUE, plugin set by default on package load to NULL, echoCmd set by default on package load to FALSE. useIntern sets the intern argument globally; legacyExec sets the legacyExec option globally, but is initialized to FALSE on unix systems (all but Windows) and TRUE on Windows; defaultFlags is initialized to NULL, but may be a character vector with values from c("quiet", "verbose") suppressEchoCmdInFunc default TRUE suppresses the effect of echoCmd within package functions, may be set FALSE for debugging.
gisBase
The directory path to GRASS binaries and libraries, containing bin and lib subdirectories among others
home
The directory in which to create the .gisrc file; defaults to $HOME on Unix systems and to USERPROFILE on Windows systems; can usually be set to tempdir()
SG
An optional SpatialGrid object to define the DEFAULT_WIND of the temporary location; if use_sp() has not been called, it will be called internally if SG is given as an object inheriting from "Spatial"; if use_sf() has been called, it will be overridden internally as only objects inheriting from "Spatial" may be given.
gisDbase
if missing, tempdir() will be used; GRASS GISDBASE directory for the working session
addon_base
if missing, assumed to be “$HOME/.grass7/addons” on Unix-like platforms, on MS Windows “%APPDATA%\GRASS7\addons”, and checked for existence
location
if missing, basename(tempfile()) will be used; GRASS location directory for the working session
mapset
if missing, basename(tempfile()) will be used; GRASS mapset directory for the working session
override
default FALSE, set to TRUE if accidental trashing of GRASS .gisrc files and locations is not a problem
use_g.dirseps.exe
default TRUE; when TRUE appears to work for WinGRASS Native binaries, when FALSE for QGIS GRASS binaries; ignored on other platforms.
pid
default as.integer(round(runif(1, 1, 1000))), integer used to identify GIS_LOCK; the value here is arbitrary, but probably should be set correctly
remove_GISRC
default FALSE; if TRUE, attempt to unlink the temporary file named in the “GISRC” environment variable when the R session terminates or when this package is unloaded
vname
A vector of GRASS file names
cat
default NULL; if not NULL, must be a logical vector matching vname, stating which (CELL) rasters to return as factor
return_format
For read_RAST(), either "SGDF" or "terra"
plugin
default taking the value set by set.pluginOption;
NULL does auto-detection, changes to FALSE if vname is longer than 1, and a sanity check will be run on raster and current region, and the function will revert to FALSE if mismatch is found; if TRUE, the plugin is available and the raster should be read in its original region and resolution; if the plugin is used, no further arguments other than mapset are respected
useGDAL
(effectively defunct, only applies to use of plugin) default taking the value set by set.useGDALOption; use plugin and readGDAL if autodetected or plugin=TRUE; or for writing writeGDAL, GTiff, and r.in.gdal, if FALSE using r.out.bin or r.in.bin
close_OK
default TRUE - clean up possible open connections used for reading metadata; may be set to FALSE to avoid the side-effect of other user-opened connections being broken
drivername
default "GTiff"; a valid GDAL writable driver name to define the file format for intermediate files
driverFileExt
default NULL; otherwise string value of required driver file name extension
return_SGDF
default TRUE returning a SpatialGridDataFrame object, if FALSE, return a list with a GridTopology object, a list of bands, and a proj4string; see example below
zcol
Attribute column number or name
NODATA
by default NULL, in which case it is set to one less than floor()of the data values, otherwise an integer NODATA value (required to be integer by GRASS r.out.bin)
overwrite
default FALSE, if TRUE inserts "overwrite" into the value of the flags argument if not already there to allow existing GRASS rasters to be overwritten
verbose
default TRUE, report how writing to GRASS is specified
layer
a layer name (string); if missing set to default of “1”
type
override type detection when multiple types are non-zero, passed to v.out.ogr
remove.duplicates
In line and area vector objects, multiple geometrical features may be associated with a single cat number, leading to duplication of data rows; this argument attempts to combine the geometrical features so that they match a single data row
with_prj
default TRUE, write ESRI-style PRJ file for transfered data
with_c
default FALSE in GRASS; if FALSE, export features with category (labeled) only; if not default, all features are exported, including GRASS “islands” which are probably spurious exterior rings filling holes.
pointDropZ
default FALSE, if TRUE, discard third coordinates for point geometries; third coordinates are alway discarded for line and polygon geometries
driver
default NULL, which will lead to the choice of the first driver found in a ordered preferred vector, currently c("SQLite", "ESRI Shapefile"); a valid OGR writable driver name to define the file format for intermediate files, one of c("GML", "SQLite"), c("ESRI_Shapefile", "MapInfo_File") is preferred as these construct the names of the intermediate files adequately
min_area
default 0.0001); Minimum size of area to be imported (square meters) Smaller areas and islands are ignored. Should be greater than snap^2
snap
default -1); Snapping threshold for boundaries (map units). '-1' for no snap
SDF
A Spatial*DataFrame to be moved to GRASS as a vector object, for SpatialPointsDataFrame, SpatialLinesDataFrame, and SpatialPolygonsDataFrame objects, or an equivalent "sf" object
v.in.ogr_flags
Character vector containing additional optional flags and/or options for v.in.ogr, particularly "o" and "overwrite"
ID
A valid DB column name for unique identifiers (optional)
remove
default TRUE, remove copied vectors created in vect2neigh
vname2
If on a previous run, remove was FALSE, the name of the temporary vector may be given to circumvent its generation
units
default “k”; see GRASS v.to.db manual page for alternatives
Note
Note that the examples use the smaller subset North Carolina location: https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.tar.gz
Author(s)
Roger Bivand
Examples
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
oechoCmd <- get.echoCmdOption()
set.echoCmdOption(TRUE)
if (run) {
print(parseGRASS("r.slope.aspect"))
}
if (run) {
doGRASS("r.slope.aspect", flags=c("overwrite"),
elevation="elevation.dem", slope="slope", aspect="aspect")
}
if (run) {
pars <- list(elevation="elevation", slope="slope", aspect="aspect")
doGRASS("r.slope.aspect", flags=c("overwrite"), parameters=pars)
}
if (run) {
print(parseGRASS("r.buffer"))
}
if (run) {
doGRASS("r.buffer", flags=c("overwrite"), input="schools", output="bmap",
distances=seq(1000,15000,1000))
}
if (run) {
pars <- list(input="schools", output="bmap", distances=seq(1000,15000,1000))
doGRASS("r.buffer", flags=c("overwrite"), parameters=pars)
}
if (run) {
set.echoCmdOption(oechoCmd)
try(res <- execGRASS("r.stats", input = "fire_blocksgg", # no such file
flags = c("C", "n")), silent=FALSE)
}
if (run) {
res <- execGRASS("r.stats", input = "fire_blocksgg", flags = c("C", "n"),
legacyExec=TRUE)
print(res)
}
if (run) {
if (res != 0) {
resERR <- execGRASS("r.stats", input = "fire_blocksgg",
flags = c("C", "n"), redirect=TRUE, legacyExec=TRUE)
print(resERR)
}
}
if (run) {
res <- stringexecGRASS("r.stats -p -l input=geology", intern=TRUE)
print(res)
}
if (run) {
stringexecGRASS(paste("r.random.cells --overwrite --quiet output=samples",
"distance=1000 ncells=100 seed=1"))
}
if (run) {
execGRASS("r.random.cells", flags=c("overwrite", "quiet"), output="samples", distance=1000,
ncells=100L, seed=1L)
}
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
run <- (run && !inherits(try(use_sp(), silent=TRUE), "try-error"))
if (run) {
G <- gmeta()
print(G)
}
if (run) {
cat(getLocationProj(), "\n")
}
if (run) {
cat(getLocationProj(g.proj_WKT=FALSE), "\n")
}
if (run) {
grd <- gmeta2grd()
print(grd)
}
if (run) {
ncells <- prod(slot(grd, "cells.dim"))
df <- data.frame(k=rep(1, ncells))
mask_SG <- sp::SpatialGridDataFrame(grd, data=df)
print(summary(mask_SG))
}
GRASS_INSTALLATION <- Sys.getenv("GRASS_INSTALLATION")
run <- FALSE
if (nzchar(GRASS_INSTALLATION)) run <- file.info(GRASS_INSTALLATION)$isdir
run <- run && require(terra, quietly=TRUE)
if (run) {
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
plot(r, col=grDevices::terrain.colors(50))
}
if (run) {
(loc <- initGRASS(GRASS_INSTALLATION, home=tempdir(), SG=r, override=TRUE))
}
if (run) {
write_RAST(r, "elev", flags="overwrite")
execGRASS("r.info", map="elev")
}
if (run) {
s <- rast(r)
values(s) <- values(r)
write_RAST(s, "elev1", flags="overwrite")
execGRASS("r.info", map="elev1")
}
if (run) {
execGRASS("r.slope.aspect", flags="overwrite", elevation="elev", slope="slope", aspect="aspect")
}
if (run) {
u1 <- read_RAST(c("elev", "slope", "aspect"), return_format="terra")
plot(u1[["elev"]], col=grDevices::terrain.colors(50))
}
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
run <- (run && !inherits(try(use_sp(), silent=TRUE), "try-error"))
GV <- Sys.getenv("GRASS_VERBOSE")
Sys.setenv("GRASS_VERBOSE"=0)
# require(rgdal)
ois <- get.ignore.stderrOption()
set.ignore.stderrOption(TRUE)
get.useGDALOption()
if (run) {
nc_basic <- readRAST(c("geology", "elevation"), cat=c(TRUE, FALSE),
useGDAL=FALSE)
nc_basic <- readRAST(c("geology", "elevation"), cat=c(TRUE, FALSE),
useGDAL=TRUE)
print(table(nc_basic$geology))
}
if (run) {
execGRASS("r.stats", flags=c("c", "l", "quiet"), input="geology")
}
if (run) {
boxplot(nc_basic$elevation ~ nc_basic$geology)
}
if (run) {
nc_basic$sqdem <- sqrt(nc_basic$elevation)
}
if (run) {
if ("GRASS" %in% rgdal::gdalDrivers()$name) {
execGRASS("g.region", raster="elevation")
dem1 <- readRAST("elevation", plugin=TRUE, mapset="PERMANENT")
print(summary(dem1))
execGRASS("g.region", raster="elevation")
}
}
if (run) {
writeRAST(nc_basic, "sqdemSP", zcol="sqdem", flags=c("quiet", "overwrite"))
execGRASS("r.info", map="sqdemSP")
}
if (run) {
execGRASS("g.remove", flags="f", name="sqdemSP", type="raster")
}
if (run) {
writeRAST(nc_basic, "sqdemSP", zcol="sqdem", useGDAL=TRUE, flags=c("quiet", "overwrite"))
execGRASS("r.info", map="sqdemSP")
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=TRUE, return_SGDF=FALSE)))
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=TRUE, return_SGDF=TRUE)))
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=FALSE, return_SGDF=TRUE)))
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=FALSE, return_SGDF=FALSE)))
}
if (run) {
str(sqdemSP)
mat <- do.call("cbind", sqdemSP$dataList)
str(mat)
}
if (run) {
print(system.time(SGDF <- sp::SpatialGridDataFrame(grid=sqdemSP$grid,
proj4string=sqdemSP$proj4string, data=as.data.frame(sqdemSP$dataList))))
}
if (run) {
summary(SGDF)
}
if (run) {
execGRASS("g.remove", flags="f", name="sqdemSP", type="raster")
execGRASS("r.mapcalc", expression="basins0 = basins - 1")
execGRASS("r.stats", flags="c", input="basins0")
}
if (run) {
basins0 <- readRAST("basins0")
print(table(basins0$basins0))
}
if (run) {
basins0 <- readRAST("basins0", plugin=FALSE)
print(table(basins0$basins0))
}
if (run) {
execGRASS("g.remove", flags="f", name="basins0", type="raster")
}
run <- run && require("terra", quietly=TRUE)
if (run) {
v1 <- read_RAST("landuse", cat=TRUE, return_format="terra")
v1
inMemory(v1)
}
if (run) {
write_RAST(v1, "landuse1", flags=c("o", "overwrite"))
execGRASS("r.stats", flags="c", input="landuse1")
execGRASS("g.remove", flags="f", name="landuse1", type="raster")
}
Sys.setenv("GRASS_VERBOSE"=GV)
set.ignore.stderrOption(ois)
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
run <- (run && !inherits(try(use_sp(), silent=TRUE), "try-error"))
GV <- Sys.getenv("GRASS_VERBOSE")
Sys.setenv("GRASS_VERBOSE"=0)
# require(rgdal)
ois <- get.ignore.stderrOption()
set.ignore.stderrOption(TRUE)
if (run) {
execGRASS("v.info", map="schools", layer="1")
}
if (run) {
print(vInfo("schools"))
schs <- readVECT("schools", plugin=NULL)
print(summary(schs))
}
if (run) {
schs1 <- readVECT("schools", plugin=FALSE)
print(summary(schs1))
}
if (run) {
writeVECT(schs, "newsch", v.in.ogr_flags=c("o", "overwrite"))
execGRASS("v.info", map="newsch", layer="1")
}
if (run) {
nschs <- readVECT("newsch")
print(summary(nschs))
}
if (run) {
print(all.equal(names(nschs), as.character(vColumns("newsch")[,2])))
}
if (run) {
names(nschs) <- paste("ABCDEFGHIJKLMNO", names(nschs), sep="")
writeVECT(nschs, "newsch1", v.in.ogr_flags=c("o", "overwrite"))
}
if (run) {
print(all.equal(names(nschs), as.character(vColumns("newsch1")[-1,2])))
}
if (run) {
nschs1 <- readVECT("newsch1")
print(all.equal(names(nschs), names(nschs1)[-1]))
}
if (run) {
print(summary(nschs1))
}
if (run) {
schs <- readVECT("schools", driver="ESRI Shapefile")
names(schs) <- paste("ABCDEFGHIJKLMNO", names(schs), sep="")
writeVECT(schs, "newsch", v.in.ogr_flags=c("o", "overwrite"),
driver="ESRI Shapefile")
print(all.equal(names(schs), as.character(vColumns("newsch")[-1,2])))
}
if (run) {
nschs <- readVECT("newsch", driver="ESRI Shapefile")
all.equal(names(schs), names(nschs)[-1])
}
if (run) {
print(vInfo("roadsmajor"))
}
if (run) {
roads <- readVECT("roadsmajor")
print(summary(roads))
}
if (run) {
cen_neig <- vect2neigh("census")
str(cen_neig)
}
if (run) {
execGRASS("g.remove", flags="f", name=c("newsch", "newsch1"), type="vector")
}
use_sf()
if (run) {
print(vInfo("schools"))
schs <- readVECT("schools", plugin=NULL)
print(summary(schs))
}
if (run) {
schs1 <- readVECT("schools", plugin=FALSE)
print(summary(schs1))
}
if (run) {
writeVECT(schs, "newsch", v.in.ogr_flags=c("o", "overwrite"))
execGRASS("v.info", map="newsch", layer="1")
}
if (run) {
nschs <- readVECT("newsch")
print(summary(nschs))
}
if (run) {
execGRASS("g.remove", flags="f", name="newsch", type="vector")
}
run <- run && require("terra", quietly=TRUE)
if (run) {
v1 <- read_VECT("census")
v1
}
if (run) {
write_VECT(v1, "census_sV")
execGRASS("v.info", map="census_sV")
}
if (run) {
execGRASS("g.remove", flags="f", name="census_sV", type="vector")
}
Sys.setenv("GRASS_VERBOSE"=GV)
set.ignore.stderrOption(ois)
if (run) use_sp()
rgrass7 documentation built on Aug. 19, 2023, 1:07 a.m.
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| rgrass7-deprecated | R Documentation |
Interface between GRASS geographical information system and R
Description
Deprecated interpreted interface between GRASS geographical information system, versions 7 and 8, and R, use rgrass instead.
Usage
execGRASS(cmd, flags = NULL, ..., parameters = NULL, intern = NULL,
ignore.stderr = NULL, Sys_ignore.stdout=FALSE, Sys_wait=TRUE,
Sys_input=NULL, Sys_show.output.on.console=TRUE, Sys_minimized=FALSE,
Sys_invisible=TRUE, echoCmd=NULL, redirect=FALSE, legacyExec=NULL)
stringexecGRASS(string, intern = NULL,
ignore.stderr = NULL, Sys_ignore.stdout=FALSE, Sys_wait=TRUE,
Sys_input=NULL, Sys_show.output.on.console=TRUE, Sys_minimized=FALSE,
Sys_invisible=TRUE, echoCmd=NULL, redirect=FALSE, legacyExec=NULL)
doGRASS(cmd, flags = NULL, ..., parameters = NULL, echoCmd=NULL,
legacyExec=NULL)
parseGRASS(cmd, legacyExec=NULL)
## S3 method for class 'GRASS_interface_desc'
print(x, ...)
getXMLencoding()
setXMLencoding(enc)
use_sf()
use_sp()
gmeta(ignore.stderr = FALSE, g.proj_WKT=NULL)
getLocationProj(ignore.stderr = FALSE, g.proj_WKT=NULL)
gmeta2grd(ignore.stderr = FALSE)
## S3 method for class 'gmeta'
print(x, ...)
get.ignore.stderrOption()
get.stop_on_no_flags_parasOption()
get.useGDALOption()
get.pluginOption()
get.echoCmdOption()
get.useInternOption()
get.legacyExecOption()
get.defaultFlagsOption()
get.suppressEchoCmdInFuncOption()
set.ignore.stderrOption(value)
set.stop_on_no_flags_parasOption(value)
set.useGDALOption(value)
set.pluginOption(value)
set.echoCmdOption(value)
set.useInternOption(value)
set.legacyExecOption(value)
set.defaultFlagsOption(value)
set.suppressEchoCmdInFuncOption(value)
initGRASS(gisBase, home, SG, gisDbase, addon_base, location, mapset,
override = FALSE, use_g.dirseps.exe = TRUE, pid, remove_GISRC=FALSE,
ignore.stderr=get.ignore.stderrOption())
get.GIS_LOCK()
set.GIS_LOCK(pid)
unset.GIS_LOCK()
unlink_.gislock()
remove_GISRC()
readRAST(vname, cat=NULL, ignore.stderr = get.ignore.stderrOption(),
NODATA=NULL, plugin=get.pluginOption(), mapset=NULL,
useGDAL=get.useGDALOption(), close_OK=TRUE, drivername="GTiff",
driverFileExt=NULL, return_SGDF=TRUE)
read_RAST(vname, cat=NULL, NODATA=NULL, ignore.stderr=get.ignore.stderrOption(),
return_format="SGDF", close_OK=return_format=="SGDF", flags=NULL)
writeRAST(x, vname, zcol = 1, NODATA=NULL,
ignore.stderr = get.ignore.stderrOption(), useGDAL=get.useGDALOption(),
overwrite=FALSE, flags=NULL, drivername="GTiff")
write_RAST(x, vname, zcol = 1, NODATA=NULL, flags=NULL,
ignore.stderr = get.ignore.stderrOption(), overwrite=FALSE, verbose=TRUE)
readVECT(vname, layer, type=NULL, plugin=NULL,
remove.duplicates = TRUE, ignore.stderr=NULL,
with_prj=TRUE, with_c=FALSE, mapset=NULL,
pointDropZ=FALSE, driver=NULL)
read_VECT(vname, layer, type=NULL, flags="overwrite",
ignore.stderr = NULL)
writeVECT(SDF, vname, v.in.ogr_flags=NULL,
ignore.stderr = NULL, driver=NULL,
min_area=0.0001, snap=-1)
write_VECT(x, vname, flags="overwrite", ignore.stderr = NULL)
vInfo(vname, layer, ignore.stderr = NULL)
vColumns(vname, layer, ignore.stderr = NULL)
vDataCount(vname, layer, ignore.stderr = NULL)
vect2neigh(vname, ID=NULL, ignore.stderr = NULL, remove=TRUE, vname2=NULL,
units="k")
Arguments
cmd |
GRASS command name |
flags |
character vector of GRASS command flags |
... |
for |
parameters |
list of GRASS command parameters, used if GRASS parameters are not given as R arguments directly; the two methods for passing GRASS parameters may not be mixed. The storage modes of values passed must match thos required in GRASS, so a single GRASS string must be a character vector of length 1, a single GRASS integer must be an integer vector of length 1 (may be an integer constant such as 10L), and a single GRASS float must be a numeric vector of length 1. For multiple values, use vectors of suitable length |
string |
a string representing one full GRASS statement, using shell syntax: command name, optionally followed by flags and parameters, all separated by whitespaces. Parameters follow the key=value format; if 'value' contains spaces, then 'value' must be quoted |
intern |
default NULL, in which case set internally from |
ignore.stderr |
default NULL, taking the value set by |
Sys_ignore.stdout, Sys_wait, Sys_input |
pass extra arguments to |
Sys_show.output.on.console, Sys_minimized, Sys_invisible |
pass extra arguments to |
echoCmd |
default NULL, taking the logical value set by |
redirect |
default |
legacyExec |
default NULL, taking the logical value set by |
x |
object |
enc |
character string to replace UTF-8 in header of XML data generated by GRASS module –interface-description output when the internationalised messages are not in UTF-8 (known to apply to French, which is in latin1) |
g.proj_WKT |
default NULL: return WKT2 representation in GRASS >= 7.6 and Proj4 in GRASS < 7.6; may be set to FALSE to return Proj4 for GRASS >= 7.6 |
value |
logical value for setting options on |
gisBase |
The directory path to GRASS binaries and libraries, containing bin and lib subdirectories among others |
home |
The directory in which to create the .gisrc file; defaults to |
SG |
An optional |
gisDbase |
if missing, |
addon_base |
if missing, assumed to be “$HOME/.grass7/addons” on Unix-like platforms, on MS Windows “%APPDATA%\GRASS7\addons”, and checked for existence |
location |
if missing, |
mapset |
if missing, |
override |
default FALSE, set to TRUE if accidental trashing of GRASS .gisrc files and locations is not a problem |
use_g.dirseps.exe |
default TRUE; when TRUE appears to work for WinGRASS Native binaries, when FALSE for QGIS GRASS binaries; ignored on other platforms. |
pid |
default |
remove_GISRC |
default FALSE; if TRUE, attempt to unlink the temporary file named in the “GISRC” environment variable when the R session terminates or when this package is unloaded |
vname |
A vector of GRASS file names |
cat |
default NULL; if not NULL, must be a logical vector matching vname, stating which (CELL) rasters to return as factor |
return_format |
For |
plugin |
default taking the value set by |
useGDAL |
(effectively defunct, only applies to use of plugin) default taking the value set by |
close_OK |
default TRUE - clean up possible open connections used for reading metadata; may be set to FALSE to avoid the side-effect of other user-opened connections being broken |
drivername |
default |
driverFileExt |
default NULL; otherwise string value of required driver file name extension |
return_SGDF |
default TRUE returning a |
zcol |
Attribute column number or name |
NODATA |
by default NULL, in which case it is set to one less than |
overwrite |
default FALSE, if TRUE inserts |
verbose |
default TRUE, report how writing to GRASS is specified |
layer |
a layer name (string); if missing set to default of “1” |
type |
override type detection when multiple types are non-zero, passed to v.out.ogr |
remove.duplicates |
In line and area vector objects, multiple geometrical features may be associated with a single cat number, leading to duplication of data rows; this argument attempts to combine the geometrical features so that they match a single data row |
with_prj |
default TRUE, write ESRI-style PRJ file for transfered data |
with_c |
default FALSE in GRASS; if FALSE, export features with category (labeled) only; if not default, all features are exported, including GRASS “islands” which are probably spurious exterior rings filling holes. |
pointDropZ |
default FALSE, if TRUE, discard third coordinates for point geometries; third coordinates are alway discarded for line and polygon geometries |
driver |
default NULL, which will lead to the choice of the first driver found in a ordered preferred vector, currently |
min_area |
default 0.0001); Minimum size of area to be imported (square meters) Smaller areas and islands are ignored. Should be greater than snap^2 |
snap |
default -1); Snapping threshold for boundaries (map units). '-1' for no snap |
SDF |
A Spatial*DataFrame to be moved to GRASS as a vector object, for SpatialPointsDataFrame, SpatialLinesDataFrame, and SpatialPolygonsDataFrame objects, or an equivalent |
v.in.ogr_flags |
Character vector containing additional optional flags and/or options for v.in.ogr, particularly "o" and "overwrite" |
ID |
A valid DB column name for unique identifiers (optional) |
remove |
default TRUE, remove copied vectors created in |
vname2 |
If on a previous run, remove was FALSE, the name of the temporary vector may be given to circumvent its generation |
units |
default “k”; see GRASS |
Note
Note that the examples use the smaller subset North Carolina location: https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.tar.gz
Author(s)
Roger Bivand
Examples
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
oechoCmd <- get.echoCmdOption()
set.echoCmdOption(TRUE)
if (run) {
print(parseGRASS("r.slope.aspect"))
}
if (run) {
doGRASS("r.slope.aspect", flags=c("overwrite"),
elevation="elevation.dem", slope="slope", aspect="aspect")
}
if (run) {
pars <- list(elevation="elevation", slope="slope", aspect="aspect")
doGRASS("r.slope.aspect", flags=c("overwrite"), parameters=pars)
}
if (run) {
print(parseGRASS("r.buffer"))
}
if (run) {
doGRASS("r.buffer", flags=c("overwrite"), input="schools", output="bmap",
distances=seq(1000,15000,1000))
}
if (run) {
pars <- list(input="schools", output="bmap", distances=seq(1000,15000,1000))
doGRASS("r.buffer", flags=c("overwrite"), parameters=pars)
}
if (run) {
set.echoCmdOption(oechoCmd)
try(res <- execGRASS("r.stats", input = "fire_blocksgg", # no such file
flags = c("C", "n")), silent=FALSE)
}
if (run) {
res <- execGRASS("r.stats", input = "fire_blocksgg", flags = c("C", "n"),
legacyExec=TRUE)
print(res)
}
if (run) {
if (res != 0) {
resERR <- execGRASS("r.stats", input = "fire_blocksgg",
flags = c("C", "n"), redirect=TRUE, legacyExec=TRUE)
print(resERR)
}
}
if (run) {
res <- stringexecGRASS("r.stats -p -l input=geology", intern=TRUE)
print(res)
}
if (run) {
stringexecGRASS(paste("r.random.cells --overwrite --quiet output=samples",
"distance=1000 ncells=100 seed=1"))
}
if (run) {
execGRASS("r.random.cells", flags=c("overwrite", "quiet"), output="samples", distance=1000,
ncells=100L, seed=1L)
}
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
run <- (run && !inherits(try(use_sp(), silent=TRUE), "try-error"))
if (run) {
G <- gmeta()
print(G)
}
if (run) {
cat(getLocationProj(), "\n")
}
if (run) {
cat(getLocationProj(g.proj_WKT=FALSE), "\n")
}
if (run) {
grd <- gmeta2grd()
print(grd)
}
if (run) {
ncells <- prod(slot(grd, "cells.dim"))
df <- data.frame(k=rep(1, ncells))
mask_SG <- sp::SpatialGridDataFrame(grd, data=df)
print(summary(mask_SG))
}
GRASS_INSTALLATION <- Sys.getenv("GRASS_INSTALLATION")
run <- FALSE
if (nzchar(GRASS_INSTALLATION)) run <- file.info(GRASS_INSTALLATION)$isdir
run <- run && require(terra, quietly=TRUE)
if (run) {
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
plot(r, col=grDevices::terrain.colors(50))
}
if (run) {
(loc <- initGRASS(GRASS_INSTALLATION, home=tempdir(), SG=r, override=TRUE))
}
if (run) {
write_RAST(r, "elev", flags="overwrite")
execGRASS("r.info", map="elev")
}
if (run) {
s <- rast(r)
values(s) <- values(r)
write_RAST(s, "elev1", flags="overwrite")
execGRASS("r.info", map="elev1")
}
if (run) {
execGRASS("r.slope.aspect", flags="overwrite", elevation="elev", slope="slope", aspect="aspect")
}
if (run) {
u1 <- read_RAST(c("elev", "slope", "aspect"), return_format="terra")
plot(u1[["elev"]], col=grDevices::terrain.colors(50))
}
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
run <- (run && !inherits(try(use_sp(), silent=TRUE), "try-error"))
GV <- Sys.getenv("GRASS_VERBOSE")
Sys.setenv("GRASS_VERBOSE"=0)
# require(rgdal)
ois <- get.ignore.stderrOption()
set.ignore.stderrOption(TRUE)
get.useGDALOption()
if (run) {
nc_basic <- readRAST(c("geology", "elevation"), cat=c(TRUE, FALSE),
useGDAL=FALSE)
nc_basic <- readRAST(c("geology", "elevation"), cat=c(TRUE, FALSE),
useGDAL=TRUE)
print(table(nc_basic$geology))
}
if (run) {
execGRASS("r.stats", flags=c("c", "l", "quiet"), input="geology")
}
if (run) {
boxplot(nc_basic$elevation ~ nc_basic$geology)
}
if (run) {
nc_basic$sqdem <- sqrt(nc_basic$elevation)
}
if (run) {
if ("GRASS" %in% rgdal::gdalDrivers()$name) {
execGRASS("g.region", raster="elevation")
dem1 <- readRAST("elevation", plugin=TRUE, mapset="PERMANENT")
print(summary(dem1))
execGRASS("g.region", raster="elevation")
}
}
if (run) {
writeRAST(nc_basic, "sqdemSP", zcol="sqdem", flags=c("quiet", "overwrite"))
execGRASS("r.info", map="sqdemSP")
}
if (run) {
execGRASS("g.remove", flags="f", name="sqdemSP", type="raster")
}
if (run) {
writeRAST(nc_basic, "sqdemSP", zcol="sqdem", useGDAL=TRUE, flags=c("quiet", "overwrite"))
execGRASS("r.info", map="sqdemSP")
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=TRUE, return_SGDF=FALSE)))
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=TRUE, return_SGDF=TRUE)))
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=FALSE, return_SGDF=TRUE)))
}
if (run) {
print(system.time(sqdemSP <- readRAST(c("sqdemSP", "elevation"),
useGDAL=FALSE, return_SGDF=FALSE)))
}
if (run) {
str(sqdemSP)
mat <- do.call("cbind", sqdemSP$dataList)
str(mat)
}
if (run) {
print(system.time(SGDF <- sp::SpatialGridDataFrame(grid=sqdemSP$grid,
proj4string=sqdemSP$proj4string, data=as.data.frame(sqdemSP$dataList))))
}
if (run) {
summary(SGDF)
}
if (run) {
execGRASS("g.remove", flags="f", name="sqdemSP", type="raster")
execGRASS("r.mapcalc", expression="basins0 = basins - 1")
execGRASS("r.stats", flags="c", input="basins0")
}
if (run) {
basins0 <- readRAST("basins0")
print(table(basins0$basins0))
}
if (run) {
basins0 <- readRAST("basins0", plugin=FALSE)
print(table(basins0$basins0))
}
if (run) {
execGRASS("g.remove", flags="f", name="basins0", type="raster")
}
run <- run && require("terra", quietly=TRUE)
if (run) {
v1 <- read_RAST("landuse", cat=TRUE, return_format="terra")
v1
inMemory(v1)
}
if (run) {
write_RAST(v1, "landuse1", flags=c("o", "overwrite"))
execGRASS("r.stats", flags="c", input="landuse1")
execGRASS("g.remove", flags="f", name="landuse1", type="raster")
}
Sys.setenv("GRASS_VERBOSE"=GV)
set.ignore.stderrOption(ois)
run <- FALSE
if (nchar(Sys.getenv("GISRC")) > 0 &&
read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") run <- TRUE
run <- (run && !inherits(try(use_sp(), silent=TRUE), "try-error"))
GV <- Sys.getenv("GRASS_VERBOSE")
Sys.setenv("GRASS_VERBOSE"=0)
# require(rgdal)
ois <- get.ignore.stderrOption()
set.ignore.stderrOption(TRUE)
if (run) {
execGRASS("v.info", map="schools", layer="1")
}
if (run) {
print(vInfo("schools"))
schs <- readVECT("schools", plugin=NULL)
print(summary(schs))
}
if (run) {
schs1 <- readVECT("schools", plugin=FALSE)
print(summary(schs1))
}
if (run) {
writeVECT(schs, "newsch", v.in.ogr_flags=c("o", "overwrite"))
execGRASS("v.info", map="newsch", layer="1")
}
if (run) {
nschs <- readVECT("newsch")
print(summary(nschs))
}
if (run) {
print(all.equal(names(nschs), as.character(vColumns("newsch")[,2])))
}
if (run) {
names(nschs) <- paste("ABCDEFGHIJKLMNO", names(nschs), sep="")
writeVECT(nschs, "newsch1", v.in.ogr_flags=c("o", "overwrite"))
}
if (run) {
print(all.equal(names(nschs), as.character(vColumns("newsch1")[-1,2])))
}
if (run) {
nschs1 <- readVECT("newsch1")
print(all.equal(names(nschs), names(nschs1)[-1]))
}
if (run) {
print(summary(nschs1))
}
if (run) {
schs <- readVECT("schools", driver="ESRI Shapefile")
names(schs) <- paste("ABCDEFGHIJKLMNO", names(schs), sep="")
writeVECT(schs, "newsch", v.in.ogr_flags=c("o", "overwrite"),
driver="ESRI Shapefile")
print(all.equal(names(schs), as.character(vColumns("newsch")[-1,2])))
}
if (run) {
nschs <- readVECT("newsch", driver="ESRI Shapefile")
all.equal(names(schs), names(nschs)[-1])
}
if (run) {
print(vInfo("roadsmajor"))
}
if (run) {
roads <- readVECT("roadsmajor")
print(summary(roads))
}
if (run) {
cen_neig <- vect2neigh("census")
str(cen_neig)
}
if (run) {
execGRASS("g.remove", flags="f", name=c("newsch", "newsch1"), type="vector")
}
use_sf()
if (run) {
print(vInfo("schools"))
schs <- readVECT("schools", plugin=NULL)
print(summary(schs))
}
if (run) {
schs1 <- readVECT("schools", plugin=FALSE)
print(summary(schs1))
}
if (run) {
writeVECT(schs, "newsch", v.in.ogr_flags=c("o", "overwrite"))
execGRASS("v.info", map="newsch", layer="1")
}
if (run) {
nschs <- readVECT("newsch")
print(summary(nschs))
}
if (run) {
execGRASS("g.remove", flags="f", name="newsch", type="vector")
}
run <- run && require("terra", quietly=TRUE)
if (run) {
v1 <- read_VECT("census")
v1
}
if (run) {
write_VECT(v1, "census_sV")
execGRASS("v.info", map="census_sV")
}
if (run) {
execGRASS("g.remove", flags="f", name="census_sV", type="vector")
}
Sys.setenv("GRASS_VERBOSE"=GV)
set.ignore.stderrOption(ois)
if (run) use_sp()
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