[R-sig-Geo] Fwd: dimensions do not match

[Paul Hiemstra]

Hi Mathieu,

As a default autoKrige deals with duplicate measurements. This is done 
by deleting one of them. It gives a warning message to the user that 
observations have been removed. This behavior can be suppressed by 
setting 'remove.duplicates = FALSE' in the call to autoKrige, now gstat 
will crash with the usual error.

cheers,
Paul

mathieu grelier wrote:
> Ok,
> I've just tried to use zerodist before calling the autoKrige function
> but the error remains the same (memory_c...).
> Did you manage to perform the local kriging? You said there was still an error.
>
> I forward this message to the author of automap.
> I don't know if automap can handle this situation.
> Paul, please could you give us an answer about last question from edzer?
>
> Thanks
> Mathieu
>
> ---------- Forwarded message ----------
> From: Edzer Pebesma <edzer.pebesma at uni-muenster.de>
> Date: 7 avr. 2008 12:42
> Subject: Re: [R-sig-Geo] dimensions do not match
> To: mathieu grelier <greliermathieu at gmail.com>, r-sig-geo at stat.math.ethz.ch
>
>
> Thanks Mathieu, for sending me the data off-line.
>
>  If you have a massive data set, you should use kriging within a local
> neighbourhood to prevent forming and inverting a covariance matrix of
> 4.3 Gb (24067 records, squared, times 8 bytes per double). You may try
> to convince the author of automap to take care of this, automatically.
>
>  When applying local kriging to your data set, I get the error message:
>
>  > k = krige(valeur~1,sitesR,mask_SG,vgm(1, "Exp",300), nmax=30)
>  [using ordinary kriging]
>
>  "chfactor.c", line 130: singular matrix in function LDLfactor()
>  Error in predict.gstat(g, newdata = newdata, block = block, nsim = nsim,  :
>   LDLfactor
>
>  which is usually, and in this case as well, due to duplicate observations, try
>
>  > zerodist(sitesR)
>
>  Does automap take care of them, and if yes how?
>  --
>  Edzer
>
>
>
>
>  mathieu grelier wrote:
>
>   
>> Ok, this is the data I use and the commands.
>> It is really weird because I use R CMD within grass and I can't
>> reproduce exactly the same error message when I follow the commands
>> directly in R.
>> This is the message I get now :
>>
>> "memory.c", line 57: can't allocate memory in function m_get()
>> Error in predict.gstat(g, newdata = newdata, block = block, nsim = nsim,  :
>>        m_get
>>
>> But, I already had this memory error when working on big datasets.
>> In the same way, I looked on the archives to see if this memory
>> problem could be solved and I didn't find anything.
>>
>> Do you know it?
>> Thanks.
>>
>> Mathieu
>>
>>
>> 2008/4/6, Edzer Pebesma <edzer.pebesma at uni-muenster.de>:
>>
>>
>>     
>>> Please send me the data as a .RData R data file, along with the steps that
>>> led to the error message.
>>>  --
>>>  Edzer
>>>
>>>  mathieu grelier wrote:
>>>
>>>
>>>
>>>       
>>>> A question about a problem already described in this list (
>>>>
>>>>
>>>>
>>>>         
>>> https://stat.ethz.ch/pipermail/r-sig-geo/2006-July/001160.html),
>>> but I
>>>
>>>
>>>       
>>>> didn't find any answer.
>>>> I am trying to achieve ordinary kriging using gstat (via the autokrige
>>>> package) in GRASS with a big dataset (24067 points).
>>>>
>>>> After the program removes duplicate data, I get the following same error :
>>>> "Error : dimensions do not match: locations 39916 and data 24067"
>>>> I don't have any NAs apparently.
>>>> Checking logfile, I could see that the error is occurring in the krige
>>>> function.
>>>>
>>>> Is there a known way to fix this problem?
>>>> Maybe I can send my data, but I don't send it for now to the list as its
>>>> weight is ~1Mo.
>>>>
>>>> Thanks
>>>> Mathieu
>>>>
>>>>       [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>>>
>>>>
>>>>         
>>>       


-- 
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: 	+31302535773
Fax:	+31302531145
http://intamap.geo.uu.nl/~paul