[R-sig-Geo] MSE

Pete Larson pslarson2 at gmail.com
Mon Dec 14 18:08:58 CET 2009


Thank you for your reply. I would like to do model comparison, but the 
cv function is just too slow for now.

Any other ideas?



Ashton Shortridge wrote:
> 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
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