[GRASS-stats] R in GRASS - v.db.addcolumn Error

Roger Bivand Roger.Bivand at nhh.no
Sat May 7 23:42:13 PDT 2016 

On Sat, 7 May 2016, Roger Bivand wrote:

> On Sat, 7 May 2016, Maximilian Bakenhus wrote:
>
>>  Okay it seems nabble really ate my content,
>>  this is the code and my grass version
>>
>>  System Info
>
> No, the output of sessionInfo() is essential, unless you know that you are 
> running rgrass7 version 0.1-7, if not, update.

On Windows, v.db.addcolumn is a batch file not an executable:

C:/Program Files/GRASS GIS 7.0.3/bin/v.db.addcolumn.bat

https://cran.r-project.org/web/packages/rgrass7/ChangeLog

shows that Windows *.bat issues were addressed in January and April this 
year, so are fixed in 0.1-7. Update rgrass7!

Roger



>
> You have:
>
>>  execGRASS("v.db.addcolumn", parameters = list(map = "sites_3", columns =
>>  "dist double precision, cats integer, xm double precision, ym double
>>  precision"))
>>  # hat den Befehl nicht gefunden, ausführung über GUI in GRASS über
>>  Befehlssuche
>
> and
>
>>   execGRASS("v.db.addcolumn",
>>             parameters = list(map = paste0('ws_', take at data$site_id),
>>                               columns = "area_sqkm double"))
>
> columns= must be a character vector; perhaps:
>
> columns=c("dist double precision", "cats integer", "xm double precision", "ym 
> double precision")
>
> This should be fairly obvious.
>
> Roger
>
>>
>>  GRASS version: 7.0.3
>>
>>  GRASS SVN Revision: 67691
>>
>>  Build Date: 2016-01-10
>>
>>  Build Platform: x86_64-w64-mingw32
>>
>>  GDAL/OGR: 1.11.3
>>
>>  PROJ.4: 4.9.2
>>
>>  GEOS: 3.5.0
>>
>>  SQLite: 3.7.17
>>
>>  Python: 2.7.5
>>
>>  wxPython: 2.8.12.1
>>
>>  Platform: Windows-8-6.2.9200
>>
>>  # Initialize GRASS
>>  loc <- initGRASS(gisBase = "C:/GRASS GIS 7.0.3",
>>                  home = tempdir(),
>>                  gisDbase = 'C:/Users/KingGoerge/Documents/GIS DataBase 2',
>>                  location = 'usa',
>>                  mapset = 'kansas-4', override = TRUE )
>>  loc
>>  # perhabs first create loaction and map before in GUI?
>>
>>  # # # read DEM
>>  execGRASS("r.in.gdal", flags = c("overwrite", "o"),
>>           parameters = list(input = 'C:/Users/KingGoerge/Documents/Gis
>>  Projekte/GIS Advanced
>>  Projekt/Höhenmodell-Kansas/20160429133734_122375530.tif',
>>                             output = "DEM"))
>>
>>  execGRASS("g.list", parameters = list(type = "rast"))
>>  # set region
>>  execGRASS("g.region", parameters = list(raster = 'DEM'))
>>  gmeta()
>> 
>> 
>>
>>  ###
>>  ----------------------------------------------------------------------------
>>  # # extract flow direction + streams from dem:
>>  execGRASS("r.watershed", flags = "overwrite",
>>           parameters = list(elevation = "DEM",
>>                             drainage = 'fdir',  # save flow direction as
>>  raster named "fdir"
>>                             stream = 'stream',  # save derived streams as
>>  raster named "stream"
>>                             threshold = 750))
>>  # list all rasters available in GRASS-Session
>>  execGRASS("g.list", parameters = list(type = "rast"))
>>  # now with fdir and stream
>> 
>> #  thin streams and convert to line and clean
>> #  thin = make stream 1pixel width
>>  execGRASS("r.thin", flags = "overwrite", parameters = list(input =
>>  'stream', output = 'stream_t'))
>>  # convert to line vector
>>  execGRASS("r.to.vect",  flags = "overwrite", parameters = list(input =
>>  'stream_t', output = 'streams', type = 'line' ))
>>  # clean vector (see help for more information)
>>  execGRASS("v.clean",  flags = c("overwrite", "c"), parameters = list(input
>>  = 'streams', output = 'streams_c', tool = 'break'))
>> 
>> 
>>
>>  # read sampling sites
>>  sites3 <- read.table('C:/Users/KingGoerge/Documents/Gis Projekte/GIS
>>  Advanced Projekt/Messpunkte_Kansas-formatiert.csv', header = TRUE, sep =
>>  ';')
>>
>>  # set coordinates to create a spatial R object
>>  coordinates(sites3) <- ~longitude + latitude
>>  plot(sites3)
>>  # write to GRASS
>>  writeVECT(sites3, "sites_3", v.in.ogr_flags = c("o", "overwrite"))
>>
>>  # list all vectors
>>  execGRASS("g.list", parameters = list(type = "vect"))
>>
>>  ## snap sites to streams
>> #  add columns to attributed table of sites
>> #  for distance id and coordinates of nearest streams,
>>  execGRASS("v.db.addcolumn", parameters = list(map = "sites_3", columns =
>>  "dist double precision, cats integer, xm double precision, ym double
>>  precision"))
>>  # hat den Befehl nicht gefunden, ausführung über GUI in GRASS über
>>  Befehlssuche
>> 
>> 
>> #  calc distance of points to nearest stream
>> #  and save distance and new coordinates to newly created columns
>>  execGRASS("v.distance",  flags = c("overwrite"),
>>           parameters = list(from = 'sites_2',
>>                             to = 'streams_c',
>>                             output = 'connectors',
>>                             upload = 'dist,cat,to_x,to_y',
>>                             column = 'dist,cats,xm,ym'))
>> 
>> #  extract new points (=snapped coordinates)
>> #  save to disc
>>  execGRASS("v.db.select", flags = c('c', 'overwrite'),
>>           parameters = list(map = 'sites_2',
>>                             columns = c('xm,ym'),
>>                             file = 'C:/Users/KingGoerge/Documents/Gis
>>  Projekte/GIS Advanced Projekt/new_points_kansas.txt'))
>>  # load from disc
>>  execGRASS("v.in.ascii", flags = c("overwrite"),
>>           parameters = list(input = 'C:/Users/KingGoerge/Documents/Gis
>>  Projekte/GIS Advanced Projekt//new_points_kansas.txt',
>>                             output = "new_sites"))
>> 
>>
>>  ###
>>  -------------------------------------------------------------------------
>>  ### Calculate catchments
>>  # read new sites
>>  snapped <- readVECT('new_sites')
>>  # copy sites_id from table to vectordata
>>  snapped at data$site_id <- sites$site_id
>>
>>  # for each Point in snapped...
>>  for (i in seq_len(nrow(snapped))) {
>>   # extract respective point
>>   take <- snapped[i,]
>>   message(paste0(i, ' out of ', nrow(snapped)))
>>   # calculate drainage area
>>   execGRASS("r.water.outlet", flags = 'overwrite',
>>             parameters = list(input = 'fdir',    # flow direction as input
>>                               output = paste0('da_', take at data$site_id),  #
>>  save as raster named "da_<site_id>" (da = drainage area)
>>                               coordinates = coordinates(take)[ ,1:2])) #
>>  coordinates of point for which drainage should be calculated
>> #  execGRASS("g.list", parameters = list(type = "rast"))
>> #  make raster to vector
>>   execGRASS("r.to.vect",  flags = 'overwrite',
>>             parameters = list(input = paste0('da_', take at data$site_id), #
>>  input = "da_<site_id>" (=raster)
>>                               output = paste0('ws_', take at data$site_id), #
>>  output = "ws_<site_id>" (=vector polygon)
>>                               type = 'area'))
>> #    execGRASS("g.list", parameters = list(type = "rast"))
>> #    execGRASS("g.list", parameters = list(type = "vect"))
>> #  Add a column 'area_sqkm' for area in sq.km to attributed table
>>   execGRASS("v.db.addcolumn",
>>             parameters = list(map = paste0('ws_', take at data$site_id),
>>                               columns = "area_sqkm double"))
>>   # calculate aresa and save to "area_sqkm" column
>>   execGRASS("v.to.db", parameters = list(
>>     map = paste0('ws_', take at data$site_id),
>>     option = 'area',
>>     columns = 'area_sqkm',  units = 'kilometers'))
>>  }
>> 
>> 
>> 
>> 
>>
>>  2016-05-06 22:11 GMT+02:00 Roger Bivand <Roger.Bivand at nhh.no>:
>> 
>> >  You have still not stated your rgrass7 version. This really is 
>> >  important,
>> >  without knowing this no help is possible. You must give much more detail 
>> >  of
>> >  what you are actually doing; make sure that rstudio is not getting in 
>> >  the
>> >  way (it runs R in separate sessions).
>> > 
>> >  * DO NOT POST IN NABBLE, IT CAN EAT CONTENT*
>> > 
>> >  Roger
>> > 
>> >  On Fri, 6 May 2016, Maximilian Bakenhus wrote:
>> > 
>> >  Hello Community,
>> > > 
>> > >  I am a german student and I work with some other students at a GRASS
>> > >  Project,
>> > >  its about watershed modeling of a DEM Projection and snap measuring 
>> > >  points
>> > >  over the new streams.
>> > >  We do this with the newest version of R Studio and GRASS 7.0.3
>> > > 
>> > >  This here is part of our code:
>> > > 
>> > > 
>> >  Where???
>> > 
>> > 
>> > 
>> > >  As we try do do the last order,
>> > >  the* v.db.addcolumn*, we retrieve this error:
>> > > 
>> > >  *Error in system(cmd0, intern = TRUE) : 'v.db.addcolumn.exe' not found
>> > >  Error in parseGRASS(cmd, legacyExec = legacyExec) :
>> > >   v.db.addcolumn not found*
>> > > 
>> > >  We really dont know, how to fix it and hope someone here does, cause 
>> > >  we
>> > >  need
>> > >  it very urgent.
>> > >  Thanks for reading,
>> > >  have a nice day
>> > > 
>> > >  Max
>> > > 
>> > > 
>> > > 
>> > > 
>> > >  --
>> > >  View this message in context:
>> > >  http://osgeo-org.1560.x6.nabble.com/R-in-GRASS-v-db-addcolumn-Error-tp5265014.html
>> > >  Sent from the Grass - Stats mailing list archive at Nabble.com.
>> > >  _______________________________________________
>> > >  grass-stats mailing list
>> > >  grass-stats at lists.osgeo.org
>> > >  http://lists.osgeo.org/mailman/listinfo/grass-stats
>> > > 
>> > 
>> >  --
>> >  Roger Bivand
>> >  Department of Economics, Norwegian School of Economics,
>> >  Helleveien 30, N-5045 Bergen, Norway.
>> >  voice: +47 55 95 93 55; fax +47 55 95 91 00
>> >  e-mail: Roger.Bivand at nhh.no
>> >  http://orcid.org/0000-0003-2392-6140
>> >  https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>> >  http://depsy.org/person/434412
>> > 
>> 
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412

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