[R-sig-Geo] MSE

Mon Dec 14 17:25:32 CET 2009

Hi Tom,

There isn't any Mean Squared Error from kriging, assuming you are using all 
the points in the model, because there are no residuals. Kriging 'honors' the 
data. You can use do cross-validation (defaults to leave one out), but this is 
pretty intensive and slow, at least in the R version (krige.cv).

Gtsat Kriging does return a variance estimate for every prediction point, the 
square root of which is often called the kriging standard error, but this is a 
measure of uncertainty at that point, rather than actual error.

Or perhaps I've completely misunderstood your question!

Ashton

On Monday 14 December 2009 06:16:20 Pete Larson wrote:
> Hello,
> 
> Is there any easy way to get the MSE from the gstat kriging fucntions?
> Or just the residuals at the measurement points?
> 
> Thanks,
> 
> Pete
> 
> Edzer J. Pebesma wrote:
> > Dear Tom,
> >
> > as your grids are spatial grids, you may want to look into the web
> > service standards of the OGC (www.opengeospatial.org) for them, WCS
> > (for reading) and WCS-T (for writing) in particular. We're
> > experimenting with this currently, using the recently open sourced
> > rasdaman software (www.rasdaman.org), which uses a data base in the
> > back end. I don't think OPeNDAP has special infrastructure for spatial
> > grids; CFNetCDF does, but by choosing this you may limit integration
> > with other software that does assume spatial data to be served over
> > OGC standards. CFNetCDF is one of the possible formats to be served
> > over WCS (and GeoTIFF etc) -- if I'm correctly informed.
> >
> > Bests,
> >
> > Stefano Casalegno wrote:
> >> Dear Tom,
> >> my best acknowledgment for the Ecogrid challenging initiative.
> >> I guess the main limitation will be "time" and this is related to
> >> the  size of grids.
> >> What is the extent of the grids ?
> >> What tool you plan to use for point 1. Overlay some point data and
> >> get the values of grids ?
> >>
> >> On a more theoretical basis,
> >> "distribution models should rely upon data that covers the whole
> >> extent of the distribution of the biota under examination"
> >>
> >> Please consider forest data from
> >> http://forest.jrc.ec.europa.eu/climate-change
> >> as supplementary predictors variables within an European
> >> biodiversity  and nature conservation application.
> >>
> >> Cheers
> >> Stefano
> >>
> >>
> >> ________________________________
> >>
> >> Stefano Casalegno, Ph.D.
> >>
> >> via Greppi 16, 21021 Angera - Italy
> >> email: stefano at casalegno.net
> >> web: http://www.casalegno.net/stefano
> >> ________________________________
> >>
> >> On Dec 13, 2009, at 6:29 PM, Tomislav Hengl wrote:
> >>> Dear R-sig-geo,
> >>>
> >>> As a part of our project (EcoGRID.nl) we have prepared some 60
> >>> thematic grids that we use as auxiliary predictors for species
> >>> distribution modeling. At this stage, we would like to put the
> >>> gridded maps (50/100 m base resolution) into some efficient
> >>> sharable geo-database.
> >>>
> >>> We will most probably put the data into the NetCDF format (http://
> >>> www.unidata.ucar.edu/software/netcdf/) because it can handle any-
> >>> dimensional array data, and because it has been in continuous
> >>> development and widespread use for many years. NetCDF grids can be
> >>> read relatively easy into R using the RNetCDF package (e.g. http://
> >>> spatial-analyst.net/DATA/readNCDF.zip). Another alternative is to
> >>> use PostGIS WKT Raster format (http://trac.osgeo.org/postgis/wiki/
> >>> WKTRaster), but this seems to be still rather experimental (?).
> >>>
> >>> Once we put the grids into NetCDF format. We plan to install
> >>> OPeNDAP (http://www.opendap.org) server on top to make the files
> >>> accessible through the web; then Geoserver (http://
> >>> www.geoserver.org) or UMN Mapserver (http://mapserver.org) to feed
> >>> a WMS from NetCDF files (raster data). Finally, we plan to add a
> >>> simple OpenLayers interface on top of that (Geoserver has it built
> >>> in) to allow direct browsing of the data and metadata (e.g. such as
> >>> this one: http://africamap.harvard.edu/)
> >>>
> >>> Just to be clear, we want to put the data on a server because we
> >>> would like to run a number of operations directly on the server
> >>> (via rgdal?):
> >>>
> >>> 1. Overlay some point data and get the values of grids (without a
> >>> need to download the grids locally);
> >>> 2. Subset/mask and resample gridded data of interest (for a given
> >>> bounding box and proj4 string; again without a need to download the
> >>> data locally);
> >>> 3. Upscale the grids from 100 m to 250, 500 m and 1 km resolution
> >>> (then download the upscaled grids).
> >>> 4. Write/upload new grids to the database (e.g. using WebDAV).
> >>> 5. Browse the grids (and metadata) via the OpenLayers.
> >>>
> >>> These are only our wishes of course. We do not know if all this is
> >>> really possible with the current software.
> >>>
> >>> Any examples or comments/suggestions/experiences are welcome
> >>> (before we start installing and testing the functionality).
> >>>
> >>> Thanx!
> >>>
> >>> Tomislav Hengl and Lourens Veen
> >>>
> >>> _______________________________________________
> >>> R-sig-Geo mailing list
> >>> R-sig-Geo at stat.math.ethz.ch
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>
> >>     [[alternative HTML version deleted]]
> >>
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-- 
Ashton Shortridge
Associate Professor			ashton at msu.edu
Dept of Geography			http://www.msu.edu/~ashton
235 Geography Building		ph (517) 432-3561
Michigan State University		fx (517) 432-1671