Re: [R-sig-Geo] New package > RStoolbox: Remote Sensing Data Analysis in R
Hi Thanks for theis. I needed this for land cover claasification for landsat 8 and hope it will be useful. I may contact you for help if required. Cheers Anand University of Mauritius On Mon, Sep 14, 2015 at 10:36 AM, Benjamin Leutner < benjamin.leut...@uni-wuerzburg.de> wrote: > Dear list members, > > We are happy to announce the initial release of our *RStoolbox* package. > RStoolbox provides various tools for remote sensing data analysis and is > now available from CRAN: >https://cran.r-project.org/web/packages/RStoolbox > > The main focus of RStoolbox is to provide a set of high-level remote > sensing tools for various classification tasks. This includes unsupervised > and supervised classification with different classifiers, fractional cover > analysis and a spectral angle mapper. Furthermore, several spectral > transformations like vegetation indices, principal component analysis or > tasseled cap transformation are available as well. > > Besides that, we provide a set of data import and pre-processing > functions. These include reading and tidying Landsat meta-data, importing > ENVI spectral libraries, histogram matching, automatic image > co-registration, topographic illumination correction and so on. > > Last but not least, RStoolbox ships with two functions dedicated to > plotting remote sensing data (*raster* objects) with *ggplot2* including > RGB color compositing with various contrast stretching options. > > RStoolbox is built on top of the *raster* package. To improve performance > some functions use embedded C++ code via the *Rcpp* package. Moreover, most > functions have built-in support for parallel processing, which is activated > by running raster::beginCluster() beforehand > > RStoolbox is hosted at www.github.com/bleutner/RStoolbox > > For a more details, including executed examples, please see > http://bleutner.github.io/RStoolbox/rstbx-docu/ > > We sincerely hope that this package may be helpful for some people and are > looking forward to any feedback, suggestions and bug reports. > > -- > Benjamin Leutner > Ned Horning > > -- > - > Benjamin Leutner M.Sc. > > Julius-Maximilians-Universität Würzburg > Institut für Geographie und Geologie > Lehrstuhl für Fernerkundung > Campus Hubland Nord -86- > 97074 Würzburg > > --- > Tel: +49-(0)931-31 89594 > Fax: +49-(0)931-31 89594-0 > eMail: benjamin.leut...@uni-wuerzburg.de > Web: http://www.fernerkundung.uni-wuerzburg.de > > ___ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > -- --- [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] help: krigged map do not show colours
Dear Jon and Roman Thanks for the reply. Im attaching the code. You may be right that the variogram may be problematic but it fitted well visually. I think also that the prediction grid was not well created. I wiould be grateful to have to hints.code how to create a useful grid and also for the spplot or other alternatives I can send more info if required. Cheers Anand On Tue, Aug 4, 2015 at 1:39 PM, Jon Skoien jon.sko...@jrc.ec.europa.eu wrote: Hi, You have attached some data, but we still dont know exactly what you do with the data (do you use the logarithm, how many bins, did you project the data set...?). However, having had a quick look using the LatLong coordinates (not really recommended), I can see that the variogram from this data set is not particularly well defined, and it could well be that you fitted a model with pure nugget effect. In that case you will get the same prediction everywhere and no color differences. Have a look at summary(map) and particularly the summary of var1.pred. You could also plot the variogram of the data together with your model, vmf, and see how they fit. I am not sure what you mean by not being able to create a prediction grid with data included. Do you mean that you want a grid which exactly overlays some of the data points? Matching one point should not be difficult, 2 and 3 should be possible, but you might get some problems with precision (FAQ 7.31). Best wishes, Jon On 8/3/2015 5:30 PM, Anand Sookun wrote: Hi Thank you Roman for your kind response. The data is as attached which is part of the whole dataset. My other problem is that im not able to create an appropriate prediction grid with some data included. The codes which failed to show colour ramps are map - krige(logcarbseq ~ 1, locations = carbon_seq, newdata = map,model = vmf) str(map) print(spplot(map, var1.pred, asp=1, col.regions=bpy.colors(64),main=OK prediction, carbon)) print(spplot(map, var1.var,col.regions=cm.colors(64),asp=1, main=OK prediction variance, carbon)) I look forward to hopefully get some solutions. Thanks again and warm regards Anand On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik roman.lust...@gmail.com wrote: What is the variability of the plotted variable? Cheers, Roman On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun asoo...@gmail.com asoo...@gmail.com wrote: Hi I have kriged my data but the map shows uniform colours - no gradual contour colour plot on map code: print(spplot(k40, var1.pred, asp=1, col.regions=bpy.colors(64),main=OK prediction, log-ppm Zn)) thnaks for any help Anand Sookun -- --- *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)* *Director cum Freelance Consultant* *Soft Sustainable Services (Mauritius)* *Research and Consultancy* Website: http://sustain-ability.webs.com/ https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- In God we trust, all others bring data. -- --- *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)* *Director cum Freelance Consultant* *Soft Sustainable Services (Mauritius)* *Research and Consultancy* Website: http://sustain-ability.webs.com/ http://sustain-ability.webs.com/ https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic ___ R-sig-Geo mailing listR-sig-Geo@r-project.orghttps://stat.ethz.ch/mailman/listinfo/r-sig-geo -- Jon Olav Skøien Joint Research Centre - European Commission Institute for Environment and Sustainability (IES) Climate Risk Management Unit Via Fermi 2749, TP 100-01, I-21027 Ispra (VA), ITALY jon.sko...@jrc.ec.europa.eu Tel: +39 0332 789205 Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission. -- --- *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)* *Director cum Freelance Consultant* *Soft Sustainable Services (Mauritius)* *Research and Consultancy* Website: http://sustain-ability.webs.com/ https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic To sig geoAug2015.R Description: Binary data vca_raster.grd Description: Binary data ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] help: krigged map do not show colours
Dear Jon I have to thank you so much for solving this issue. I did't notice that there was a projection and grid problem. I hope I would be able to move forward with my analysis with R and perhaps still need your kind and much appreciated help. Cheers Anand On Wed, Aug 5, 2015 at 12:08 PM, Jon Skoien jon.sko...@jrc.ec.europa.eu wrote: Good. For the next function, I think you are trying to use an sp-function (gridded) on a raster object. You can convert between these, but not necessarily use the same functions. Use spgrid = rasterToPoints(YourRaster, spatial = TRUE) gridded(spgrid) = TRUE if you want to convert your raster layer to a spatial object. Best wishes, Jon On 8/5/2015 10:00 AM, Anand Sookun wrote: Dear John Thanks again. this time it worked but the variogram is not plotting well and some other problems croped. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘gridded’ for signature ‘RasterLayer I will try by looking closely at the scripts and be back to you soon Best Wishes Anand On Wed, Aug 5, 2015 at 11:36 AM, Jon Skoien jon.sko...@jrc.ec.europa.eu wrote: Dear Anand On 8/5/2015 9:03 AM, Anand Sookun wrote: Dear John Greetings I really appreciate your help. Itried what you proposed but got stuck with the following: proj4string(carbon_seq) - CRS(+init=epsg 4326) # epsg-code for latlong Error in CRS(+init=epsg 4326) : no colon in init= string Sorry, there is a : missing, should be CRS(+init=epsg:4326) See if it works better! Jon Also I TRIED AGAIN proj4string(carbon_seq) - CRS(+init=epsg4326) # epsg-code for latlong Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘proj4string-’ for signature ‘data.frame, CRS I tried with rgdal but got the same eror require(rgdal) Loading required package: rgdal rgdal: version: 0.8-16, (SVN revision 498) Geospatial Data Abstraction Library extensions to R successfully loaded Loaded GDAL runtime: GDAL 1.10.1, released 2013/08/26 Path to GDAL shared files: C:/Users/Anand/Documents/R/win-library/3.0/rgdal/gdal GDAL does not use iconv for recoding strings. Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480] Path to PROJ.4 shared files: C:/Users/Anand/Documents/R/win-library/3.0/rgdal/proj im attacing the gri file. Thanks for your time. CHEERS ANAND On Tue, Aug 4, 2015 at 4:55 PM, Jon Skoien jon.sko...@jrc.ec.europa.eujon.sko...@jrc.ec.europa.eu wrote: Anand, I could not open your .grd file in R, I think the .gri file is missing. However, looking at it in a text editor, and comparing with your R-script, it seems something went wrong with your projections. Your .csv-file has LatLong coordinates, but you are setting the projection to +proj=utm +zone=40 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0, the same as you seem to have in your prediction raster. But you need to reproject your observations in this case. # First set the right projection: proj4string(carbon_seq) - CRS(+init=epsg4326) # epsg-code for latlong # Then transform carbon_seq = spTransform(carbon_seq, CRS(+proj=utm +zone=40 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0)) If you do this, your prediction grid should overlap your observations, and the colors should reflect your color ramp. What you essentially did before was to make a prediction thousands of km away from your observations, and then all values will be the same. Best wishes, Jon On 8/4/2015 12:48 PM, Anand Sookun wrote: Dear Jon and Roman Thanks for the reply. Im attaching the code. You may be right that the variogram may be problematic but it fitted well visually. I think also that the prediction grid was not well created. I wiould be grateful to have to hints.code how to create a useful grid and also for the spplot or other alternatives I can send more info if required. Cheers Anand On Tue, Aug 4, 2015 at 1:39 PM, Jon Skoien jon.sko...@jrc.ec.europa.eu mailto:jon.sko...@jrc.ec.europa.eu wrote: Hi, You have attached some data, but we still dont know exactly what you do with the data (do you use the logarithm, how many bins, did you project the data set...?). However, having had a quick look using the LatLong coordinates (not really recommended), I can see that the variogram from this data set is not particularly well defined, and it could well be that you fitted a model with pure nugget effect. In that case you will get the same prediction everywhere and no color differences. Have a look at summary(map) and particularly the summary of var1.pred. You could also plot the variogram of the data together with your model, vmf, and see how they fit. I am not sure what you mean by not being able to create a prediction grid with data included. Do you mean that you want a grid which
Re: [R-sig-Geo] help: krigged map do not show colours
Hi Thank you Roman for your kind response. The data is as attached which is part of the whole dataset. My other problem is that im not able to create an appropriate prediction grid with some data included. The codes which failed to show colour ramps are map - krige(logcarbseq ~ 1, locations = carbon_seq, newdata = map,model = vmf) str(map) print(spplot(map, var1.pred, asp=1, col.regions=bpy.colors(64),main=OK prediction, carbon)) print(spplot(map, var1.var,col.regions=cm.colors(64),asp=1, main=OK prediction variance, carbon)) I look forward to hopefully get some solutions. Thanks again and warm regards Anand On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik roman.lust...@gmail.com wrote: What is the variability of the plotted variable? Cheers, Roman On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun asoo...@gmail.com wrote: Hi I have kriged my data but the map shows uniform colours - no gradual contour colour plot on map code: print(spplot(k40, var1.pred, asp=1, col.regions=bpy.colors(64),main=OK prediction, log-ppm Zn)) thnaks for any help Anand Sookun -- --- *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)* *Director cum Freelance Consultant* *Soft Sustainable Services (Mauritius)* *Research and Consultancy* Website: http://sustain-ability.webs.com/ https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- In God we trust, all others bring data. -- --- *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)* *Director cum Freelance Consultant* *Soft Sustainable Services (Mauritius)* *Research and Consultancy* Website: http://sustain-ability.webs.com/ https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic Lat,Lon,DCO2_Xpowr 57.4623,-20.1761,11.06449137 57.4938,-20.1628,12.30966604 57.5147,-20.1791,9.763761194 57.5135,-20.1634,9.907643355 57.5065,-20.1484,10.5670516 57.5385,-20.1694,9.838228196 57.5305,-20.1001,9.548338451 57.5573,-20.1171,7.809539255 57.5993,-20.1509,6.679576196 57.5674,-20.184,7.127874261 57.6036,-20.1257,8.265899517 57.5865,-20.0463,8.210560118 57.5753,-20.159,9.335306993 57.5667,-20.0743,7.818804659 57.5763,-20.1031,9.449380721 57.6265,-20.096,8.332084482 57.5923,-20.0699,9.688198548 57.5297,-20.0628,9.290967463 57.5431,-20.1272,10.08502632 57.5493,-20.0682,6.939564654 ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Re: [R-sig-Geo] help: krigged map do not show colours
DearJon Thnaks. I will try that soon. Cheers Anand On Tue, Aug 4, 2015 at 4:55 PM, Jon Skoien jon.sko...@jrc.ec.europa.eu wrote: Anand, I could not open your .grd file in R, I think the .gri file is missing. However, looking at it in a text editor, and comparing with your R-script, it seems something went wrong with your projections. Your .csv-file has LatLong coordinates, but you are setting the projection to +proj=utm +zone=40 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0, the same as you seem to have in your prediction raster. But you need to reproject your observations in this case. # First set the right projection: proj4string(carbon_seq) - CRS(+init=epsg4326) # epsg-code for latlong # Then transform carbon_seq = spTransform(carbon_seq, CRS(+proj=utm +zone=40 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0)) If you do this, your prediction grid should overlap your observations, and the colors should reflect your color ramp. What you essentially did before was to make a prediction thousands of km away from your observations, and then all values will be the same. Best wishes, Jon On 8/4/2015 12:48 PM, Anand Sookun wrote: Dear Jon and Roman Thanks for the reply. Im attaching the code. You may be right that the variogram may be problematic but it fitted well visually. I think also that the prediction grid was not well created. I wiould be grateful to have to hints.code how to create a useful grid and also for the spplot or other alternatives I can send more info if required. Cheers Anand On Tue, Aug 4, 2015 at 1:39 PM, Jon Skoien jon.sko...@jrc.ec.europa.eu mailto:jon.sko...@jrc.ec.europa.eu wrote: Hi, You have attached some data, but we still dont know exactly what you do with the data (do you use the logarithm, how many bins, did you project the data set...?). However, having had a quick look using the LatLong coordinates (not really recommended), I can see that the variogram from this data set is not particularly well defined, and it could well be that you fitted a model with pure nugget effect. In that case you will get the same prediction everywhere and no color differences. Have a look at summary(map) and particularly the summary of var1.pred. You could also plot the variogram of the data together with your model, vmf, and see how they fit. I am not sure what you mean by not being able to create a prediction grid with data included. Do you mean that you want a grid which exactly overlays some of the data points? Matching one point should not be difficult, 2 and 3 should be possible, but you might get some problems with precision (FAQ 7.31). Best wishes, Jon On 8/3/2015 5:30 PM, Anand Sookun wrote: Hi Thank you Roman for your kind response. The data is as attached which is part of the whole dataset. My other problem is that im not able to create an appropriate prediction grid with some data included. The codes which failed to show colour ramps are map - krige(logcarbseq ~ 1, locations = carbon_seq, newdata = map,model = vmf) str(map) print(spplot(map, var1.pred, asp=1, col.regions=bpy.colors(64),main=OK prediction, carbon)) print(spplot(map, var1.var,col.regions=cm.colors(64),asp=1, main=OK prediction variance, carbon)) I look forward to hopefully get some solutions. Thanks again and warm regards Anand On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik roman.lust...@gmail.com mailto:roman.lust...@gmail.com wrote: What is the variability of the plotted variable? Cheers, Roman On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun mailto:asoo...@gmail.comasoo...@gmail.com mailto:asoo...@gmail.com wrote: Hi I have kriged my data but the map shows uniform colours - no gradual contour colour plot on map code: print(spplot(k40, var1.pred, asp=1, col.regions=bpy.colors(64),main=OK prediction, log-ppm Zn)) thnaks for any help Anand Sookun -- --- *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)* *Director cum Freelance Consultant* *Soft Sustainable Services (Mauritius)* *Research and Consultancy* Website: http://sustain-ability.webs.com/ https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org mailto:R-sig-Geo@r-project.org https://stat.ethz.ch
[R-sig-Geo] help: krigged map do not show colours
Hi I have kriged my data but the map shows uniform colours - no gradual contour colour plot on map code: print(spplot(k40, var1.pred, asp=1, col.regions=bpy.colors(64),main=OK prediction, log-ppm Zn)) thnaks for any help Anand Sookun -- --- *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)* *Director cum Freelance Consultant* *Soft Sustainable Services (Mauritius)* *Research and Consultancy* Website: http://sustain-ability.webs.com/ https://www.linkedin.com/profile/view?id=161468467trk=nav_responsive_tab_profile_pic [[alternative HTML version deleted]] ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
