execGRASS: Run GRASS commands

In rgrass7: Interface Between GRASS 7 Geographical Information System and R

Description

The functions provide an interface to GRASS commands run through system, based on the values returned by the --interface description flag using XML parsing. If required parameters are omitted, and have declared defaults, the defaults will be used.

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)
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)

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
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 to be printed
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)

Details

parseGRASS checks to see whether the GRASS command has been parsed already and cached in this session; if not, it reads the interface description, parses it and caches it for future use. doGRASS assembles a proposed GRASS command with flags and parameters as a string, wrapping parseGRASS, and execGRASS is a wrapper for doGRASS, running the command through system (from 0.7-4, the ... argument is not used for passing extra arguments for system). The command string is termed proposed, because not all of the particular needs of commands are provided by the interface description, and no check is made for the existence of input objects. Support for multiple parameter values added with help from Patrick Caldon. Support for defaults and for direct use of GRASS parameters instead of a parameter list suggested by Rainer Krug.

Value

parseGRASS returns a GRASS_interface_desc object, doGRASS returns a character string with a proposed GRASS command - the expanded command name is returned as an attribute, and execGRASS returns what system or system2 return, particularly depending on the intern argument when the character strings output by GRASS modules are returned. If intern is FALSE, system returns the module exit code, while system2 returns the module exit code with “resOut” and “resErr” attributes.

Note

If any package command fails with a UTF-8 error from the XML package, try using setXMLencoding to work around the problem that GRASS modules declare –interface-description output as UTF-8 without ensuring that it is (French is of 6.4.0 RC5 latin1).

Author(s)

Roger S. Bivand, e-mail: [e-mail]

See Also

system

Examples

if (nchar(Sys.getenv("GISRC")) > 0 &&
  read.dcf(Sys.getenv("GISRC"))[1,"LOCATION_NAME"] == "nc_basic_spm_grass7") {
  oechoCmd <- get.echoCmdOption()
  set.echoCmdOption(TRUE)
  print(parseGRASS("r.slope.aspect"))
  doGRASS("r.slope.aspect", flags=c("overwrite"),
    elevation="elevation.dem", slope="slope", aspect="aspect")
  pars <- list(elevation="elevation", slope="slope", aspect="aspect")
  doGRASS("r.slope.aspect", flags=c("overwrite"), parameters=pars)
  print(parseGRASS("r.buffer"))
  doGRASS("r.buffer", flags=c("overwrite"), input="schools", output="bmap",
    distances=seq(1000,15000,1000))
  pars <- list(input="schools", output="bmap", distances=seq(1000,15000,1000))
  doGRASS("r.buffer", flags=c("overwrite"), parameters=pars)
  set.echoCmdOption(oechoCmd)
  try(res <- execGRASS("r.stats", input = "fire_blocksgg", # no such file
    flags = c("C", "n")), silent=FALSE)
  res <- execGRASS("r.stats", input = "fire_blocksgg", flags = c("C", "n"),
    legacyExec=TRUE)
  print(res)
  if (res != 0) {
    resERR <- execGRASS("r.stats", input = "fire_blocksgg", 
      flags = c("C", "n"), redirect=TRUE, legacyExec=TRUE)
    print(resERR)
  }
}

Example output

Loading required package: sp
Loading required package: XML
GRASS GIS interface loaded with GRASS version: (GRASS not running)

rgrass7 documentation built on May 2, 2019, 5:55 p.m.