Re: [GRASS-user] Boxplots based on raster data in GRASS GIS
If you ran execGRASS("g.extension", extension="r.boxplot", operation="add"),
the add-on will not be found until you restart the R session in RStudio
(parseGRASS caches all *.bat found the first time it is used on Windows). GRASS
extensions are installed in GRASS, not R, but can be installed through
execGRASS(). In that case, on Windows, the R session needs to restarted. In any
case, I guess that making the boxplot in R is easier, see for example:
https://rsbivand.github.io/rgrass/reference/readRAST.html.
--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
roger.biv...@nhh.no
From: sibylle.stoec...@gmx.ch
Sent: 24 April 2024 11:45
To: Roger Bivand; grass-user@lists.osgeo.org
Subject: RE: [GRASS-user] Boxplots based on raster data in GRASS GIS
Yes I have installed successfully all addons (visualised in the figure below).
Additionally I was able to run the code using GUI or GRASS GIS command.
* Managed installed GRASS addons extensions: then r.boxplot is visible as
installed.
As g.region, r.mask, v.to.rast is working and the error was just related to
r.boxplot, I was wondering if I need to install addons a second time in rstudio?
[cid:image001.png@01DA963C.F15DEE40]
-----Original Message-
From: Roger Bivand
Sent: Wednesday, April 24, 2024 10:25 AM
To: grass-user@lists.osgeo.org
Cc: sibylle.stoec...@gmx.ch
Subject: Re: [GRASS-user] Boxplots based on raster data in GRASS GIS
It is a GRASS addon, install as per:
https://grass.osgeo.org/download/addons/<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgrass.osgeo.org%2Fdownload%2Faddons%2F=05%7C02%7CRoger.Bivand%40nhh.no%7C53695f68bf734e3c848208dc64435092%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638495487507664917%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=AjIgJKpSmV8LCwwqvw1Co7pDm819QpI5uXJiPCEOufg%3D=0>
https://grass.osgeo.org/grass83/manuals/g.extension.html<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgrass.osgeo.org%2Fgrass83%2Fmanuals%2Fg.extension.html=05%7C02%7CRoger.Bivand%40nhh.no%7C53695f68bf734e3c848208dc64435092%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638495487507677612%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=l2K7Z617o9mAPK1yqlGOraOJWz76%2Fmjyd%2Bq9j2L03LA%3D=0>
https://grass.osgeo.org/grass83/manuals/addons/r.boxplot.html<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgrass.osgeo.org%2Fgrass83%2Fmanuals%2Faddons%2Fr.boxplot.html=05%7C02%7CRoger.Bivand%40nhh.no%7C53695f68bf734e3c848208dc64435092%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638495487507686606%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=WXu7btmERlnCeIsqL2ubiFKtqDmnZVNZnf6RnNpdKac%3D=0>
--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
roger.biv...@nhh.no<mailto:roger.biv...@nhh.no>
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Re: [GRASS-user] Boxplots based on raster data in GRASS GIS
It is a GRASS addon, install as per: https://grass.osgeo.org/download/addons/ https://grass.osgeo.org/grass83/manuals/g.extension.html https://grass.osgeo.org/grass83/manuals/addons/r.boxplot.html -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway roger.biv...@nhh.no ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Using RStudio in a GRASS GIS session
First tell us exactly what you do. Do you start GRASS first (how was GRASS installed, which version?), then what? The first message suggests a failed GRASS installation. Can you use GRASS at all? Try to run any regular example on the data in your location in GRASS to check that GRASS works before anything else. --- Roger Bivand Emeritus Professor Department of Economics Norwegian School of Economics, Bergen, Norway Fra: sibylle.stoec...@gmx.ch Sendt: fredag, april 19, 2024 5:56:04 p.m. Til: Roger Bivand Kopi: grass-user@lists.osgeo.org Emne: RE: [GRASS-user] Using RStudio in a GRASS GIS session Dear community Dear Roger I suppose it is my name Here the output from the console: C:\Users\Sibylle Stöckli> C:\Users\Sibylle Stöckli> ERROR: Unable to read WIND file: not enough values to unpack (expected 2, got 1) library(rgrass) Der Befehl "library" ist entweder falsch geschrieben oder konnte nicht gefunden werden. Kind regards Sibylle -Original Message----- From: Roger Bivand Sent: Friday, April 19, 2024 4:31 PM To: sibylle.stoec...@gmx.ch Cc: grass-user@lists.osgeo.org Subject: Re: [GRASS-user] Using RStudio in a GRASS GIS session Please see: https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frsbivand.github.io%2Frgrass%2Farticles%2Fuse.html=05%7C02%7CRoger.Bivand%40nhh.no%7C04d6d2c547b14550ec5f08dc608936de%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638491389645818206%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=3fLYSzCE3uRNBetqb69RxZz%2FzLiv%2F1LuBFkdb%2B19nsA%3D=0<https://rsbivand.github.io/rgrass/articles/use.html>. https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Frsbivand.github.io%2Frgrass%2Farticles%2Fuse.html=05%7C02%7CRoger.Bivand%40nhh.no%7C04d6d2c547b14550ec5f08dc608936de%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638491389645826443%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=zM%2Fia4%2BGNTgKd%2Bjxo3HVJnDgt02JrI9CSyx%2F1AtwK%2FU%3D=0<https://rsbivand.github.io/rgrass/articles/use.html> Do you have a GRASS location and wish to use R on the data in that location? Then start GRASS first and start rstudio from inside GRASS. The error messages suggest that something is missing in your installation. Is your query related to https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fr-help%2F2024-April%2F479232.html=05%7C02%7CRoger.Bivand%40nhh.no%7C04d6d2c547b14550ec5f08dc608936de%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638491389645832105%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=i1bTT5y7lmJcG1MtEniurDJsEYbK63t0UB%2BSagiLmMM%3D=0<https://stat.ethz.ch/pipermail/r-help/2024-April/479232.html> ? -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway roger.biv...@nhh.no ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Using RStudio in a GRASS GIS session
Please see: https://rsbivand.github.io/rgrass/articles/use.html. https://rsbivand.github.io/rgrass/articles/use.html Do you have a GRASS location and wish to use R on the data in that location? Then start GRASS first and start rstudio from inside GRASS. The error messages suggest that something is missing in your installation. Is your query related to https://stat.ethz.ch/pipermail/r-help/2024-April/479232.html ? -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway roger.biv...@nhh.no ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] grass-7.8.5 on Fedora 33
I install from source, so cannot check. PROJ 7 needs Tiff and curl (to access the CDN) over and above the sqlite3 requirement introduced by PROJ 6. Is the install process pulling in PROJ > 6? I see 6.3.2 as the F33 current version, but >= 7 would explain complaints about missing Tiff: $ pkg-config proj --libs --static -L/usr/local/lib -lproj -lsqlite3 -ltiff -lcurl -lstdc++ - Roger Bivand NHH Norwegian School of Economics, Bergen, Norway -- Sent from: http://osgeo-org.1560.x6.nabble.com/Grass-Users-f3884509.html ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] [R-sig-Geo] [R] Need help using GRASS within R - error when running the script for a second time
Dear Loïc, On Wed, 8 Jul 2020, Loïc Valéry wrote: Dear Roger, Following the message you left on github this morning (here is the github link to make it easier for the subscribers to follow our exchanges: https://github.com/rsbivand/rgrass7/issues/13#issuecomment-655384113), I continued my investigations and I finally found the origin of the problem. First of all, I would like to answer your questions this morning: - OS: Windows 8.1 - R version 3.6.3 - all the packages are up to date - the GRASS version: stand-alone Windows GRASS 7.8.3 - I confirm that when I load the library rgrass7, R returns a message indicating that GRASS is not open. Coming back to the subject itself, when you told me that you were unable to reproduce the problem under Windows, I also did the test and, indeed, when I only ran these few lines of code, everything worked fine and I could execute initGRASS() as many times as I wanted without any problems. But these few lines of code are included in a larger script that first calls link2GI to interface R with the OTB software. And this is where the problem occurs. Here are the results of the tests in a very synthetic way: So perhaps raise the issue with link2GI? https://github.com/r-spatial/link2GI/ Or separate the components to run in different R sessions as a stop-gap? It is quite likely that attaching link2GI will overwrite GRASS environment variables (and the reverse is probably the case too). Roger Test 1: 1-Running initGRASS() n times: everything works fine n times 2-Running link2GI::linkOTB() 3-Running initGRASS() : this crashes on the first attempt. Test 2: 1-Running link2GI::linkOTB() 2-Running initGRASS() n times: everything works fine n times 3-Running link2GI::linkOTB() 4-Running initGRASS() : this crashes on the first attempt. There is clearly a conflict between these two packages: running the command link2GI::linkOTB() seems to "break" the link made by rgrass7 between R and GRASS. So, I modified the code to prevent the problem from occurring during a second run of the script. But even though I had no problems since then, it's still a "band-aid on a wooden leg". It would be nice if Chris could find a solution to prevent linkOTB() from breaking the link between R and GRASS. I hope this feedback is clear and remain at your disposal to complete this message if you would like more information. Best regards, Loïc De : R-sig-Geo de la part de Loïc Valéry Envoyé : mardi 7 juillet 2020 21:03 À : roger.biv...@nhh.no Cc : grass-user ; r-sig-...@r-project.org Objet : Re: [R-sig-Geo] [R] Need help using GRASS within R - error when running the script for a second time Dear Roger, Sorry for cross-posting. As you invite me, I'm going to post my case on https://github.com/rsbivand/rgrass7/issues. Just a short comment to yours: if the reason you give is the right one, I don't understand why the script works the first time but not the second time. In your hypothesis, I guess it shouldn't work at all. Best regards, Loïc De : Roger Bivand Envoyé : mardi 7 juillet 2020 20:20 À : Loïc Valéry Cc : Micha Silver ; r-sig-...@r-project.org ; grass-user Objet : Re: [R-sig-Geo] [R] Need help using GRASS within R - error when running the script for a second time Please do not cross-post between lists, because few are likely to subscribe to both. Choose rather to post only to the list likely to include people using R and GRASS: http://lists.osgeo.org/mailman/listinfo/grass-stats Further, please post plain text only - I missed your earlier post to grass-user because it was scrubbed as HTML (or maybe Micha's reply). Once resolved, you might report back on grass-user and R-sig-geo on the findings. Briefly, it looks as though you are caught in the transition in sp/rgdal and sf from Proj4 to WKT2-2019 CRS, and similar changes in Grass. Grass 7.8 and R packages may be installed with old PROJ/GDAL or new PROJ/GDAL. So far, nobody knows how to use g.proj and siblings sensibly in the R context. Most likely, using the wkt= parameter when the object in R has a WKT2 representation is going to be much more secure than passing a proj4= string, but wkt= takes a file name or standard input. I would invite discussion in an issue on: https://github.com/rsbivand/rgrass7/issues with use cases (platform-independent). Roger On Tue, 7 Jul 2020, Loïc Valéry wrote: Dear all, As advised by Micha (FYI his reply is at the end of this email) , I contact you to submit an inextricable problem when using rgrass7 : the script (cf. just below) works the first time but, when I rerun it a second time, R and windows return error messages. For this to work, I must close and open R or use the rs.restartR() command from RStudio, which is not very convenient because it stops the script. Many thanks in advance for your help. Loïc @Micha : thank you very much for your reply. But I performed the tests
Re: [GRASS-user] [R-sig-Geo] [R] Need help using GRASS within R - error when running the script for a second time
atialPolygonsDataFrame
features : 31
extent : 477371.3, 477397.6, 5631995, 5632020 (xmin, xmax, ymin, ymax)
crs : +proj=utm +zone=32 +datum=WGS84 +units=m +no_defs
variables : 1
names : Seg_ID
min values : 1
max values : 31
Warning message:
In proj4string(x) : CRS object has comment, which is lost in output
# initialization of GRASS 7.8 from R
initGRASS(gisBase ="C:/Program Files/GRASS GIS 7.8",
home="temp/GRASS",gisDbase="temp/GRASS", use_g.dirseps.exe=F,remove_GISRC=T, override=T)
gisdbase temp/GRASS
location file19685026c56
mapset file196829fa7141
rows 1
columns 1
north 1
south 0
west 0
east 1
nsres 1
ewres 1
projection NA
I suspect that the problem comes from 'projection NA' when initializing GRASS
(cf. just above)
What you need to do here is setup the CRS of your new location.
Typically, you would run initGRASS and point to a *previously created*
LOCATION, with CRS already defined. In this case, since you are creating
a new location, you must define it's coordinate system. (GRASS is very
"picky" about that).
Here's a GIS Stackexchange post that explains:
https://gis.stackexchange.com/questions/183032/create-a-new-grass-database-in-r-with-crs-projection
You can derive the full proj4 string from your sp object with:
p4str = sp::proj4string(seg_poly)
Then use that to set the project parameters for the new LOCATION, with
execGRASS("g.proj", flags = "c", proj4 = p4str) Now you should be able
to continue with...
execGRASS("v.generalize",flag=c("overwrite"),parameters=list(input="vec1",
+
output="GRASS_smooth_seg_poly",
+
error="GRASS_smooth_seg_poly_error",
+
method="distance_weighting",
+ threshold=1))
As a novice in the field, I would be very grateful for your help.
I remain at your entire disposal for any further information you may need to
help me in finding a solution to this problem.
Yours sincerely,
Loïc
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Re: [GRASS-user] rgrass7 syntax for passing a command
Simply, don't.
execGRASS() is for executing single GRASS commands, not a drop-in
replacement for bash.
Try something like creating the point in R with the correct projection, and
write that vector object to your mapset:
library(sp)
library(rgrass7)
pt <- SpatialPointsDataFrame(matrix(c(636645, 218835), ncol=2),
proj4string=CRS(paste(execGRASS("g.proj", flags="j", intern=TRUE),
collapse=" ")),
data=data.frame(x=1))
writeVECT(pt, "outlet")
You could create a temporary text file to read in:
tf <- tempfile()
writeLines("636645, 218835", tf)
execGRASS("v.in.ascii", input=tf, output="outlet1", separator=",",
flags="n")
which is closer to your script but less natural.
Yes, grass-stats is a more appropriate list.
Roger
-
Roger Bivand
NHH Norwegian School of Economics, Bergen, Norway
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[GRASS-user] Re: Natural breaks classification
Since all Spatial*DataFrame objects behave link data.frame objects, you can say: DTM- readRAST6(DTM@mapset, ignore.stderr=TRUE) DTM_class - classIntervals(DTM.df$varOfInterest, n=5, style=fisher) However, if nrow(DTM) is large, you may find that the natural breaks classifications take a lot of time, because the number of possible alternative classifications to compare is very large. If you can reasonably represent the distribution of your variable of interest by a sample, do that, but add back the maximum and minimum values. Of course, in this case you may get different class intervals for each sample. In spearfish, I see: library(spgrass6) spear - readRAST6(c(geology, elevation.dem), cat=c(TRUE, FALSE), + useGDAL=TRUE) library(classInt) system.time(CI0 - classIntervals(spear$elevation.dem, n=5, style=fisher)) user system elapsed 1151.1360.053 1153.775 nrow(spear) [1] 294978 CI0 style: fisher [1066,1221.5) [1221.5,1338.5) [1338.5,1472.5) [1472.5,1608.5) [1608.5,1840] 93972 60419 59562 45228 33136 set.seed(1) system.time(CI1 - classIntervals(c(sample(na.omit(spear$elevation.dem), 500), + range(na.omit(spear$elevation.dem))), n=5, style=fisher)) user system elapsed 0.017 0.002 0.019 CI1 style: fisher [1066,1215.5) [1215.5,1322.5) [1322.5,1450) [1450,1591) [1591,1840] 159 109 86 78 70 table(findInterval(na.omit(spear$elevation.dem), CI0$brks, all.inside=TRUE)) 1 2 3 4 5 88747 59755 57077 47726 39012 Or for more precision: set.seed(1) var_na - na.omit(spear$elevation.dem) mm_var - range(var_na) out - vector(mode=list, length=100) system.time(for (i in seq(along=out)) out[[i]] - classIntervals(c(sample(var_na, 500), mm_var), n=5, style=fisher)) user system elapsed 0.312 0.000 0.316 mbrks - sapply(out, [[, brks) str(mbrks) num [1:6, 1:100] 1066 1216 1322 1450 1591 ... apply(mbrks, 1, mean) [1] 1066.000 1218.920 1337.745 1473.920 1612.390 1840.000 which gives a result very like the one using the complete data set but taking over three orders of magnitude longer, using 100 samples of 500 raster cells each. Hope this helps, Roger Salvatore Mellino wrote Hi, thanks a lot. Now the process started, but the operation DTM_class - classIntervals(DTM.df$varOfInterest, n=5, style=fisher takes too long; it was started by hours but does not end. Is it normal? Salvatore Il giorno 16/mag/2012, alle ore 22:04, Luigi Ponti ha scritto: On 16/05/2012 21:10, Luigi Ponti wrote: On 16/05/2012 20:55, Salvatore Mellino wrote: I'm trying but I receive an error. 1. In R I started the libraries spgarass6 and classInt 2. I imported the DTM in R using DTM- readRAST6(DTM@mapset, ignore.stderr=TRUE) 3. I used the commandDTM_class- classIntervals(DTM, n=5, style=fisher) and I received the error Error in classIntervals(DTM, n = 5, style = fisher) : var is not numeric I do not recall exactly, but it may be that classIntervals does not have a method for spatial data frames (i.e. the output of readRAST6). One thing I would try to get the breaks anyway, is a regular R data.frame, for example: DTM.df - as.data.frame(DTM) DTM_class - classIntervals(DTM.df, n=5, style=fisher) I am replying to myself as I may have omitted part of the answer -- my apologies. Start the same way: DTM.df - as.data.frame(DTM) then get variable names: names(deltaYieldVector.df) then use the variable of interest (altitude, I guess): DTM_class - classIntervals(DTM.df$varOfInterest, n=5, style=fisher) This should work; we were feeding a data.frame as input to classIntervals, whereas a variable is needed (e.g. one of the variables in the data.frame). Let me know how it goes. Kind regards, Luigi ___ grass-user mailing list grass-user@.osgeo http://lists.osgeo.org/mailman/listinfo/grass-user -- View this message in context: http://osgeo-org.1560.n6.nabble.com/Natural-breaks-classification-tp4975148p4975552.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] Re: spgrass6
Just 2k may mean 4 million rectangles. R display is vector, hard-copy, with some recent support for raster grids when the rectangles are in fact square. As has been said, the graphics engine is not designed for fast screen output, but for scientific statistical graphics. spplot uses lattice graphics, which are slower anyway, but analytically more powerful. For me running levelplot() - the internals of spplot - on a 2k by 2k matrix takes 2 seconds, but output to a png file using cairo takes 70 seconds. Using the improved raster graphics handling for square cells with image() rather than spplot() and useRaster=TRUE - equivalent to image.SpatialGridDataFrame() and useRasterImage=TRUE with the same matrix takes 1.2 seconds on x11/cairo. You didn't say which version of R you are using - the raster graphics facilities have been improved recently. Did you try using image() instead of spplot() if your cells are square, and if rasterImage() is available in your version of R? Roger Paolo Cavallini wrote Il 22/02/2012 12:21, Benjamin Ducke ha scritto: As opposed to GRASS, R has not been designed with computational and/or memory efficiency as a priority. Oh! I was not fully aware of this. Maybe your analysis would allow you to run your computations on a representative sample instead of the whole dataset? In our case, the analysis is vert simple: just ssplot() of a small (2k by 2k cells) raster. Thanks. -- Paolo Cavallini See: http://www.faunalia.it/pc ___ grass-user mailing list grass-user@.osgeo http://lists.osgeo.org/mailman/listinfo/grass-user -- View this message in context: http://osgeo-org.1560.n6.nabble.com/spgrass6-tp4494142p4495201.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] Re: readVECT6 in R under GRASS
You need to provide a lot more information, including the messages displayed when spgrass6 (and possibly rdgal) are loaded, and the output of sessionInfo(). These will tell us which versions you are using. Then also run: execGRASS(g.list, parameters=list(type=vect)) to check that the vector object you think that you have is actually visible. It may be in a mapset that is not on your search path. Roger Salvatore Mellino wrote: Hi, I'm trying to open a vector file (points) in GRASS with R. I used the following command: rain - readVECT6(rain_2010, ignore.stderr=TRUE) but I received the following message: Error in ogrInfo(dsn = dsn, layer = layer, input_field_name_encoding = input_field_name_encoding) : Cannot open layer How can I fix the problem? Thanks. Salvatore ___ grass-user mailing list grass-user@.osgeo http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://osgeo-org.1803224.n2.nabble.com/readVECT6-in-R-under-GRASS-tp6924585p6924616.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] Re: Error running GRASS from R
There is a specific list for R/GRASS questions: http://lists.osgeo.org/mailman/listinfo/grass-stats. I don't know how you you started the R session. I hope you started R within a running GRASS session, as you seem to be using an existing location. You mention using initGRASS() which you should never do with an existing location, unless you really know what you are doing. You do not say whether you have also used the execGRASS() wrapper from R to run the other commands, or whether these were run from the command line. More information is needed - such as does the same script work locally, or when run without the remote desktop access on the faster computer. Roger Tim Besser wrote: Dear GRASS-community, I have a very strange problem. I created a script in R (2.10.1) for the preparation of my datasets which work fine on my laptop (winxp). I use the spgrass6 package and GRASS 6.4.1. As the script would run for days on my old laptop I now got a remote desktop connection to a much faster computer at the university (win7). However, while cmds like r.reclass or r.in.gdal work on that computer the r.patch cmd produces following error: execGRASS(r.patch, flags=c(z), parameters=list(input=mangroves_1989_138_044_LR_recl,mangroves_1989_138_045_UL_recl,mangroves_1989_138_045_UR_recl, output=testomat), intern=T) Error in system(cmd0, intern = TRUE) : Createprocess konnte 'C:\GRASS6~1.1\bin\RPATCH~1.EXE --interface-description' nicht ausführen Fehler in parseGRASS(cmd) : r.patch not found I checked the GRASS directory and it is set right in the initGRASS command. I hope you can help me with one. I have no clue what to do! Thanks in advance, Tim ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://osgeo-org.1803224.n2.nabble.com/Error-running-GRASS-from-R-tp6598521p6599623.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] Re: Installing spgrass6 package - Errors and warnings
... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/usr/local/lib/R/site-library/XML’ ERROR: dependencies ‘rgdal’, ‘XML’ are not available for package ‘spgrass6’ * removing ‘/usr/local/lib/R/site-library/spgrass6’ The downloaded packages are in ‘/tmp/RtmpP2fUan/downloaded_packages’ Warning messages: 1: In install.packages(spgrass6, dependencies = TRUE) : installation of package 'rgdal' had non-zero exit status 2: In install.packages(spgrass6, dependencies = TRUE) : installation of package 'XML' had non-zero exit status 3: In install.packages(spgrass6, dependencies = TRUE) : installation of package 'spgrass6' had non-zero exit status The result is I am not able to use spgrass. library(spgrass6) Error in library(spgrass6) : there is no package called 'spgrass6' As an intermediate level user in terms of commands and also regarding R and GRASS packages I am not able to decide what went wrong. Can you please help me out. Regards, Chethan S. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://osgeo-org.1803224.n2.nabble.com/Installing-spgrass6-package-Errors-and-warnings-tp5522860p5523163.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] Re: Download the new release 6.4.0
Hamish: Are you (or more likely the OSGeo4W developers) aware of: http://cran.r-project.org/doc/manuals/R-admin.html#Building-R-for-64_002dbit-Windows which is now up and running nicely? Roger hamish-2 wrote: kapo coulibaly wrote: Is there a 64 bit version for windows? unfortunately not- until our build toolchain (minGW, Msys, osgeo4w) supports it, or we release grass 7 which is free from some of those shackles, we're pretty much stuck at 32 bit on Windows. If you have to work with massive datasets, perhaps installing e.g. Ubuntu 64bit in a VirtualBox virtual machine inside Vista/Windows7 64 bit could get you going?(?) Either that or find a Mac or Linux to work on. :-/ my guess is that mingw and co. will get 64 bit before too long though. obviously there's demand for it. Hamish ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://osgeo-org.1803224.n2.nabble.com/Download-the-new-release-6-4-0-tp5517558p5523173.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] Retaining holes in buffers
On Mon, 25 Jan 2010, Hamish wrote: Roger wrote: PS. Where is v.to.rast on the wx menu system? in the wx GUI try: Help - Show menu tree then Search: [command] then type in v.to.rast Regretably, on my 6.4.0RC5, there are only GRASS GIS Help, GRASS GIS GUI Help, and About GRASS GIS to choose from. or have a look in the module synopsis PDF http://grass.osgeo.org/gdp/grassmanuals/grass64_module_list.pdf Yes, that is: File Map type conversions Vector to raster I'd been looking under Vector for obvious reasons. Thanks, Roger there is an open wish to add the menu location between the option summary and the description.html part of the module help pages. It's doable, it just takes some Makefile magic. Hamish -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: roger.biv...@nhh.no ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] R and GRASS-windows (readRAST6 problem, installation)
For questions of this kind, please use the statgrass list. When you repeat your question on that list, please include sessionInfo() with all information including your locale, and full GRASS details, that is what GRASS version, how installed (there are many different variants, which version of the standalone installer), how used (Rterm.exe, Rgui.exe, ...), from which terminal R was started, and verbatim output of gmeta6(). Using spaces in path variables is never a good idea anyway, but it might be possible to add an extra layer of protection. Without knowing your exact system specifications will however make your report difficult to reproduce. Roger Martin Maier-2 wrote: Hello at all I use R to do statistics of some GRASS data. On the windows machines (XP and W2K) there occurred a problem when using the readRAST6 command form the spgrass6 library. I think the problem is linked to the standard installation of the GRASS standalone installer. The standalone installer creates a folder named GIS DataBase under My Documents. To test where the problem is, I moved the folder GIS DataBase to D:\ Now I started R from within the new GRASS wxpython GUI. Within R I loaded spgrass6 (library(spgrass6)). Then the command readRAST6 fails. After renaming GIS DateBase to GISDataBase (and of course new start of GRASS and R) everything with the readRAST6 command works fine. So my guess is, that the readRAST6 command can not handle the blanks in the paths and on the other hand the installation of GRASS under windows with the standalone installer creates a default GIS database with a blank in the folder name. So probably it would be a good idea to change GIS DataBase to GISDataBase. But then there is still the blank in My Documents! Can anyone confirm this, and should I file a bug report? Martin ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://n2.nabble.com/R-and-GRASS-windows-readRAST6-problem-installation-tp3932646p3935041.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] R and GRASS (readVECT6 problem)
The last time this was seen, it was a locale problem. I heard today something from that questioner, who asked on the more relevant statsgrass list. Try setting your locale to an English one. I'll try to release the package with a patch, although the original questioner did not report success (but that could be because he was unable to install a source package). Roger Martin Maier-2 wrote: Hi, I am using the latest GRASS windows binary (WinGRASS-6.4.0SVN-r39626-1-Setup.exe) on W2K. My R version is 2.9.2. After starting R from within GRASS, loading the library(spgrass6) it is not possible to use the readVECT6 command (with the South-Dakota dataset) in R: map - readVECT6(bugsites) Error in vInfo(vname) : Vector information not found readRAST6() and gmeta6() both works fine. Does anybody have the same error and can give a hint, why this error occures? Martin ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://n2.nabble.com/R-and-GRASS-readVECT6-problem-tp3913174p3915521.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] problem on vectorizing a float point raster
I think that r.to.vect wants to build a line structure, like river channels, but sees all the raster cells occupied, so no linear structure, and the advice to thin first is then appropriate. If this is connected to your question about calculating a measure of spatial autocorrelation for the raster data, then I suspect that you do not need polygons but rather points, where r.out.xyz may be helpful, followed by v.in.ascii if you will be using GRASS downstream, or if you want to emit a shapefile for GeoDa (another posting). If you really want to calculate a measure of spatial autocorrelation for your raster, I suggest copying the raster to R with readRAST6, creating the neighbour list with dnearneigh() with max. distance the greater of ewres and nsres, and proceeding from there in the usual way. But please consider the inevitable fact that unless the resolution of your raster matches the natural support of the phenomenon of interest, the observed autocorrelation will certainly be driven by your having multiple neighbouring observations of each entity, in addition to not having demeaned (detrended) the data. This means that any results will almost certainly be spurious. Hope this helps, Roger Milton Cezar Ribeiro wrote: Dear Grass-Gurus, I have a 2400x2200 raster image with values ranging from 0.1 to 42, in float format. Now I need vetororize the image, on the way that each pixel come to be a polygon and the pixel value be stored as attribute. I am trying to do this using: r.to.vect input=temp71.img output=temp71_img_integer_vect_200m --o -b but grass return the following error messages: GRASS 6.4.0svn (newLocation):C:/GRASS-6-SVN/msys/home/mjfortin r.to.vect inpu t=temp71.img output=temp71_img_integer_vect_200m --o -b WARNING: Vector map temp71_img_integer_vect_200m already exists and will be overwritten WARNING: Table temp71_img_integer_vect_200m linked to vector map temp71_img_integer_vect_200m does not exist Extracting lines... ERROR: Raster map is not thinned properly. Please run r.thin. By the way, I am running grass under a WinXp 64bit. Any help are welcome. Cheers milton brazil=toronto ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://n2.nabble.com/problem-on-vectorizing-a-float-point-raster-tp3052124p3054013.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] problem on vectorizing a float point raster
The other thread was on the openspace list and was concerned with calculating local Moran's Ii. My comments there copied here for completeness: In your case, temperature will be being driven by altitude at least, and possibly other important omitted variables. I also think that you will find exploratory variography on the (detrended) data, or perhaps rather a sample of the data (about 4M observations), might give some information. But I don't think that squeezing your data into an inappropriate methods setting is going to help much, and I'm pretty certain that just comparing the output of a function of your input data and GRASS r.neighbors average values for increasing values of the size parameter would be sufficient to display the local dependence, most of which will still be driven by the trend. For example in spearfish: g.region rast=elevation.dem r.univar -g map=elevation.dem # to get the mean and variance values r.mapcalc 'demean_elev=elevation.dem-1353.66931789804' r.neighbors -c input=demean_elev output=demean_elev3 method=average size=3 r.mapcalc 'Ii=(demean_elev*demean_elev3)/31343.402316476' Then compare histograms and displays of Ii for increasing values of size. Roger Roger Bivand wrote: I think that r.to.vect wants to build a line structure, like river channels, but sees all the raster cells occupied, so no linear structure, and the advice to thin first is then appropriate. If this is connected to your question about calculating a measure of spatial autocorrelation for the raster data, then I suspect that you do not need polygons but rather points, where r.out.xyz may be helpful, followed by v.in.ascii if you will be using GRASS downstream, or if you want to emit a shapefile for GeoDa (another posting). If you really want to calculate a measure of spatial autocorrelation for your raster, I suggest copying the raster to R with readRAST6, creating the neighbour list with dnearneigh() with max. distance the greater of ewres and nsres, and proceeding from there in the usual way. But please consider the inevitable fact that unless the resolution of your raster matches the natural support of the phenomenon of interest, the observed autocorrelation will certainly be driven by your having multiple neighbouring observations of each entity, in addition to not having demeaned (detrended) the data. This means that any results will almost certainly be spurious. Hope this helps, Roger Milton Cezar Ribeiro wrote: Dear Grass-Gurus, I have a 2400x2200 raster image with values ranging from 0.1 to 42, in float format. Now I need vetororize the image, on the way that each pixel come to be a polygon and the pixel value be stored as attribute. I am trying to do this using: r.to.vect input=temp71.img output=temp71_img_integer_vect_200m --o -b but grass return the following error messages: GRASS 6.4.0svn (newLocation):C:/GRASS-6-SVN/msys/home/mjfortin r.to.vect inpu t=temp71.img output=temp71_img_integer_vect_200m --o -b WARNING: Vector map temp71_img_integer_vect_200m already exists and will be overwritten WARNING: Table temp71_img_integer_vect_200m linked to vector map temp71_img_integer_vect_200m does not exist Extracting lines... ERROR: Raster map is not thinned properly. Please run r.thin. By the way, I am running grass under a WinXp 64bit. Any help are welcome. Cheers milton brazil=toronto ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - Roger Bivand Economic Geography Section Department of Economics Norwegian School of Economics and Business Administration Helleveien 30 N-5045 Bergen, Norway -- View this message in context: http://n2.nabble.com/problem-on-vectorizing-a-float-point-raster-tp3052124p3054112.html Sent from the Grass - Users mailing list archive at Nabble.com. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] Re: GRASS R : g.region command not found
Milton Cezar Ribeiro miltinho.astronauta at gmail.com writes: Dear all, I am running grass65 under MSYS under Vista. After launch MSYS / GRASS / R, I get the information about mapset without problem. But as my raster image are very large, R can support the file. But when I try run system(g.region ...) I get error on R. May be R can't get the PATH where the g.region command are. You must add .exe to compiled commands, and .bat to scripts. Wait for a forthcoming 0.6-* series spgrass6, which will automate some of this. For questions like this, do use the statgrass list. Roger PS. Don't use Windows if you need to do real work - there are so many binary GRASS versions that interfacing them all is a nightmare (see the pain on OSGEO4W)! ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-stats] Re: [GRASS-user] Testing i.pca ~ prcomp(), m.eigensystem ~ princomp()
On Tue, 10 Mar 2009, Nikos Alexandris wrote: On Tue, 2009-03-03 at 14:26 +0100, Nikos Alexandris wrote: On Tue, 2009-03-03 at 13:18 +0100, Markus Neteler wrote: On Tue, Mar 3, 2009 at 12:26 PM, Hamish hamis...@yahoo.com wrote: ... it will be really good to finally have all this documented. I find it hard to follow these long mails. Why not enjoying the GRASS Wiki to stabilize the documentation and comparisons? Markus Yes, why not? Hmmm, you mean to put these stuff already in the Wiki before we are sure about the one last and very important variable (=eigenvalues reported by i.pca)? Kind regards, Nikos I've started the PCA grass-wiki page. I am trying to build it... step by step. Expert advice is always welcome and highly appreciated. http://grass.osgeo.org/wiki/Principal_Component_Analysis Good, thanks. There you say that you are using some MODIS surface reflectance products. I guess it will be easier to check things if the data (GRASS location) are available, so that others can try the same calculations. Would it be possible to make one or more test sets available, and link them from thw Wiki? Roger Kind regards, Nikos ___ grass-stats mailing list grass-st...@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-stats -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: roger.biv...@nhh.no ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] Re: Using R to check points in polygons does not work
Corrado ct529 at york.ac.uk writes: Dear friends, Platform: Ubuntu 7.10, Grass 6.2.3,PostgresSQL 8.2,R 2.6.2 Yes, I am in a hurry. If I do not solve it by tomorrow, then it is back to ARCGIS I am afraid. It is not my will, of course, but the project's leader is already not keen on switching to GRASS, so she is pressing for me to solve it using ARCGIS. :( However it goes, good luck! In any case, please keep notes, because at speed it's easy to mix up either species, or conservation areas (or both). I'm pretty certain overlay() on the points and polygons will give you what you need, first for the straight polygons, then for their buffers. Roger ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-stats] Re: [GRASS-user] grass/stats mapping/prediction question
On Wed, 19 Dec 2007, Dylan Beaudette wrote: On Wednesday 19 December 2007, Roger Bivand wrote: On Wed, 19 Dec 2007, Daniel McInerney wrote: The original questioner should have written to the grass-stats list in the first place - thanks for CC-ing. See below for inline comments: Hi Andy, I am unsure how to then move the 'outmap' back across to grass. How can i convert the df to a spatial grid object. AFAIK, 'predict' won't create a dataframe object. R should return FALSE for is.data.frame(outmap) and TRUE for is.numeric(outmap) You can slot the model output to the AttributeList of It hasn't been an AttributeList for a long time - the data slot *is* a data frame. We *always* need the output of sessionInfo() to help - update.packages() is most often very helpful too. one of the SpatialGridDataFrames that you created when you read in a GRASS raster and then use writeRAST6 to write it back to GRASS. e.g. using 'anmax' from your example anmax$anmax - outmap #if that doesn't work, you might try anmax$anmax - as.numeric(outmap) writeRAST6(anmax, NameOfNewGRASSRaster, anmax) Regards, Daniel. cc: [EMAIL PROTECTED] andrew haywood wrote: Dear List, I am having some problems analysing some ecoligical models in grass using the spgrass package through R. I have 130 plot locations where i have observed presence/absence of a species. I have followed a similar framework to the BUGSITE modelling example from Markus's 2003 grass gis handouts (Grass 5) I have no problems constructing the model based on the 130 plots and the environmental layers from grass. See the OSGeo tutorial September 2006: http://www.foss4g2006.org/contributionDisplay.py?contribId=46sessionId=59; confId=1 and the OSGeo Journal note: http://www.osgeo.org/files/journal/final_pdfs/OSGeo_vol1_GRASS-R.pdf for more up-to-date information. However, I am having problems bringing all the maps through into R so I can make a prediction map. The region isnt too large 1600 by 800 cells at 10m resolution I can bring all the environmental layers through to R using readRAST6() which doesnt take too much time at all. However i assume I must convert the spatial grid objects into dataframes to apply the predicted model function. No, usually not at all, since the objects have a data.frame in the data slot, and have the standard access methods. So I then coerce them into dataframes using as.dataframe (this takes ages) I then merge all the dataframes into a single dataframe. (this takes ages) I then apply the model predict to the new data frame. I am unsure how to then move the 'outmap' back across to grass. How can i convert the df to a spatial grid object. Im thinking i must be doing something wrong. As it quite quick to pull through the layers . But seems to take quite a lot of processing to get the layers into a datframe appropppriate for applying the predictions. Any help would be greatly appreciated. Andy # pull through environmental layers # FAST anmax - readRAST6(anmax, ignore.stderr=TRUE) anmin - readRAST6(anmin, ignore.stderr=TRUE) aspect - readRAST6(aspect, ignore.stderr=TRUE) dem10_lidar - readRAST6(dem10_lidar, ignore.stderr=TRUE) Wrong, do: mydata - readRAST6(c(anmax, anmin, aspect, dem10_lidar), ignore.stderr=TRUE) then the data slot of the object is a data frame. Look at summary(mydata) for a sanity check. # coerce to dataframe # SLOW mypred_anmaxDF-as.data.frame(anmax) mypred_anminDF-as.data.frame(anmin) mypred_aspectDF-as.data.frame(aspect) mypred_dem10_lidarDF-as.data.frame(dem10_lidar) # merge into single dataframe # VERY SLOW merge_tmp-merge(mypred_anmaxDF,mypred_anminDF) rm(mypred_anmaxDF,mypred_anminDF) merge_tmp1-merge(merge_tmp,mypred_aspectDF) rm(merge_tmp,mypred_aspectDF) mypredDF-merge(merge_tmp1,mypred_dem10_lidarDF) #apply model What is tree? You may need to do extra steps depending on what class(tree) says - if you have used rpart() or some such, you may find that outmap - predict(tree,newdata=mydata, type=class) works, or outmap - predict(tree,newdata=as(mydata, data.frame), type=class) Maybe just assign into mydata straight away: mydata$outmap - predict(tree,newdata=as(mydata, data.frame), type=class) given ?predict.rpart saying: If 'type=class': (for a classification tree) a factor of classifications based on the responses. which looks like a vector for a vector response in the formula to rpart(). But do check what happens if there are NA in the newdata, because the default predict() behaviour may be to drop those observations. Look at summary(mydata). Some formula-using model fitting functions just work, like lm() and the predict() method for lm objects. From there, as Daniel wrote: writeRAST6(mydata, rpartpred, outmap) Hope this helps, Roger outmap - predict(tree,newdata=mypredDF, type=class) An article on this in the OSGeo newsletter might be a nice way to document simple modeling examples with GRASS and R
[GRASS-user] Re: Start R w/in Cygwin and Native WinGrass?
paallen at attglobal.net writes: Hi all, I use window for my work computers so I have been using Grass under Cygwin and the latest native WinGrass and R for windows. By the way the WinGrass RC3 look GREAT I want to use the R package spgrass6. Can/How do I start windows R within cygwin and WinGrass? Use a console interface - under cygwin I usually start an xterm within the GRASS session, then start R within that (either Rgui or Rterm). You may need to set .libPaths() within R, and may also need to check the working directory in Rgui, depending on environment variable settings. Roger Thanks Phil Sent via BlackBerry by ATT ___ grass-user mailing list grass-user at lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
