[R-sig-Geo] passing 'cutoff' to the 'autoKrige' function ('automap' package)

[Paul Hiemstra]

Hi,

The miscFitOptions parameter does not include the 'variogram' paramters. 
I will look into adding them, together with the option to set the 
boundaries manually. However, autofitVariogram at this stage defines a 
fixed set of boundaries, so I'm not sure if the parameters you mention 
will resort any effect even when passing them on. An option at this 
stage would be to use the normal krige function combined with 
autofitVariogram. autofitVariogram passes on parameters to variogram() 
using the ... .

Could you create a new issue in the bitbucket.org account which stores 
automap [1]? This way I can keep track of the issues that need to be 
fixed for autofitVariogram.

cheers,
Paul

[1] https://bitbucket.org/paulhiemstra/automap/issues/new

On 03/25/2011 08:57 AM, Mauricio Zambrano wrote:
> Dear list,
>
> Is there any way to pass the 'cutoff' argument (or 'width', or other
> arguments of the 'variogram' function of the 'gstat' package)  to the
> 'autoKrige' function of the 'automap' package ?
>
> I tried with:
>
>    
>> x.ok<- autoKrige(zinc~1, meuse, meuse.grid, miscFitOptions=list(maxdist=100,  cutoff=500, width=50) )
>>      
> but both arguments are ignored.
>
>
> I also tried with:
>
>    
>> x.ok<- autoKrige(zinc~1, meuse, meuse.grid, maxdist=100,  cutoff=500, width=100)
>>      
> but I got the following error message:
>
> "Error in gstat(formula = formula, data = locations, model = model,
> beta = beta,  :
>   unused argument(s) (cutoff = 500, width = 50)"
>
>
> Some session info:
>
> R version 2.12.2 (2011-02-25)
> automap_1.0-9
> gstat_0.9-79
>
>
> Here there is a reproducible example (for the 'autofitVariogram'
> function, because I didn't find a way to pass the 'cutoff' and 'with'
> arguments to the 'autoKrige' function):
>
> ------------ START ---------------
>
> library(automap)
>
> # Data preparation
> data(meuse)
> coordinates(meuse) =~ x+y
> data(meuse.grid)
> gridded(meuse.grid) =~ x+y
>
> # Computing the 'boundaries' value for the 'variogram' function,
> # in order to properly compare its results with those of the
> 'autofitVariogram' function
>
> input_data<- meuse
>
> x<- coordinates(input_data)[, 1]
> y<- coordinates(input_data)[, 2]
> scale_number<- (0.35 * sqrt((max(x) - min(x))^2 + (max(y) - min(y))^2)/100)
> boundaries<- c(2, 4, 6, 9, 12, 15, 25, 35, 50, 65, 80, 100) * scale_number
>
> # variogram computation. Case 1, default parameters
> vgm.gstat<- variogram(zinc ~ 1, locations=meuse, boundaries=boundaries)
> vgm.automap<- autofitVariogram(zinc ~ 1, input_data=meuse)
>
> # These variograms are the same
> print(vgm.gstat)
> print(vgm.automap$exp_var)
>
> # variogram computation. Case 2, with 'cutoff' and 'width'
> vgm.gstat2<- variogram(zinc ~ 1, locations=meuse, cutoff=500, width=50)
> vgm.automap2<- autofitVariogram(zinc ~ 1, input_data=meuse,
> cutoff=500, width=50)
>
> # These variograms are NOT the same
> print(vgm.gstat2)
> print(vgm.automap2$exp_var)
>
> # variogram computation. Case 3, with 'cutoff', 'width' and 'boundaries'
> vgm.gstat3<- variogram(zinc ~ 1, locations=meuse, cutoff=500,
> width=50, boundaries=boundaries)
> vgm.automap3<- autofitVariogram(zinc ~ 1, input_data=meuse,
> cutoff=500, width=50)
>
> # These variograms are the same
> print(vgm.gstat3)
> print(vgm.automap3$exp_var)
>
>
> ------------ END ---------------
>
>
> Looking at the examples, I think that the problem arises because the
> 'boundaries' argument superimpose its values to the 'cutoff' one, both
> in the 'variogram' and 'autofitVariogram' functions.
>
> However, whereas in the 'variogram' function the boundaries are
> optional, in the 'autofitVariogram' they are computed internally (in a
> smart way), but its maximum default value disable any shorter 'cutoff'
> passed to the 'autofitVariogram' function.
>
>
> In any case, I think that even after solving the issue related to
> 'cutoff' and 'boundaries', it will still be impossible to pass the
> 'cutoff' argument to the 'autoKrige' function, because the '...'
> argument in 'autoKrige' is passed (internally) to the 'krige' function
> and not to 'autofitVariogram' one. Am I right ?
>
> I'm not sure if this could be considered a bug, but I thought it could
> be useful to report this behaviour, for the next release of 'automap'.
>
>
> Kind regards,
>
> Mauricio Zambrano B.
>
>
>    


-- 
Paul Hiemstra, MSc
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 253 5773
http://intamap.geo.uu.nl/~paul
http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770

currently @ KNMI
paul.hiemstra_AT_knmi.nl