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about ST kriging

5 messages · Pınar Aslantas Bostan, Edzer Pebesma

Pınar Aslantas Bostan
# 
Dear all,

I am working about space-time kriging. Before I asked again about ST kriging
but now the problem is 
different and I could not overcome it!

During kriging operation I got this error:
Error in chol.default(A$Sm, LINPACK = TRUE) : 
  non-positive definite matrix in 'chol'

I explained the data set below:

# prec is annual precipitation measured from 257 meteorological stations

# w is STSDF object
Object of class STSDF
[[Spatial:]]
Object of class SpatialPoints
Coordinates:
         min     max
Xnew  140556 1730472
Ynew 4309064 4971309
Is projected: NA 
proj4string : [NA]
Number of points: 257
[[Temporal:]]
     Index                      object at time  
 Min.   :1970-01-01 12:00:00   Min.   : 1.0  
 1st Qu.:1979-07-03 00:00:00   1st Qu.:10.5  
 Median :1989-01-01 12:00:00   Median :20.0  
 Mean   :1989-01-01 02:46:09   Mean   :20.0  
 3rd Qu.:1998-07-03 00:00:00   3rd Qu.:29.5  
 Max.   :2008-01-01 12:00:00   Max.   :39.0  
[[Data attributes:]]
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  114.5   413.7   533.6   633.0   735.6  3332.0 

# I used grid to obtain predictions over it. It has 25 km spatial resolution

# time is temporal entity of study. It contains 39 annual observation.

# index is required for STSDF, and I used this code to create index.
as.integer(as.factor(data$Year)))

# v is space-time variogram

How can I solve the problem?
Thank you in advance!


Pinar Aslantas Bostan
Research Assistant
Department of Geodetic and
Geographic Information Technologies (GGIT) Middle East Technical University
06531 Ankara/TURKEY
aslantas at metu.edu.tr
1 day later
Edzer Pebesma
# 
Hi Pinar,

it is not clear which variogram model you pass, or how your data are
laid out in space and time.

Possible causes for a non-positive definite covariance matrix include:

- a variogram model with (nearly) perfect correlation
- duplicate observations (observations having identical location AND time)
- an invalid variogram model

A small, reproducible example (data + script) would help identify the
problem.

Best regards,
--
Edzer
On 09/20/2011 11:15 AM, P?nar Aslantas Bostan wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Pınar Aslantas Bostan
    

    

      
      #
    

  


  

      
Hi Edzer,

Thank you very much for your mail. I found two records have identical location, but it is not my fault because I checked the original source data and it is erroneous. 

Now I have another problem; R gives another error message:
Error: cannot allocate vector of size 95.4 Mb

My computer includes 32-bit Windows and  3,5 GB RAM. I am not sure if I install 64-bit Windows, then the problem is solved? Or maybe I should minimize the data. Do you have any idea about it?

Best wishes,
Pinar

-----Original Message-----
From: r-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-project.org] On Behalf Of Edzer Pebesma
Sent: Wednesday, September 21, 2011 3:46 PM
To: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] about ST kriging

Hi Pinar,

it is not clear which variogram model you pass, or how your data are
laid out in space and time.

Possible causes for a non-positive definite covariance matrix include:

- a variogram model with (nearly) perfect correlation
- duplicate observations (observations having identical location AND time)
- an invalid variogram model

A small, reproducible example (data + script) would help identify the
problem.

Best regards,
--
Edzer

        
On 09/20/2011 11:15 AM, P?nar Aslantas Bostan wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Edzer Pebesma
    

    

      
      #
    

  


  

      
Pinar, what are the dimensions (space and time) of your data, i.e. what
does dim(w) return?

Have you tried kriging with a (spatial and/or temporal) subset?

        
On 09/22/2011 01:38 PM, P?nar Aslantas Bostan wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Pınar Aslantas Bostan
    

    

      
      #
    

  


  

      
Edzer, I have 256 meteorological station and 39 year value.

            

      
      
      
    

        
[1] 256  39   1

Before I tried only spatial kriging and I did not get memory.size error. Just a moment ago, I used another computer (64-bit Windows and 6 GB RAM), again I got the same error. 

-----Original Message-----
From: Edzer Pebesma [mailto:edzer.pebesma at uni-muenster.de] 
Sent: Thursday, September 22, 2011 2:47 PM
To: P?nar Aslantas Bostan
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] about ST kriging

Pinar, what are the dimensions (space and time) of your data, i.e. what
does dim(w) return?

Have you tried kriging with a (spatial and/or temporal) subset?

        
On 09/22/2011 01:38 PM, P?nar Aslantas Bostan wrote: