[R] issues with krige function
Adrienne Wootten
amwootte at ncsu.edu
Wed Oct 31 16:48:19 CET 2012
Thierry, To answer your first question
summary(casedata)
station year month day obs
mpe
Length:236 Min. :2011 Min. :8 Min. :28 Min.
:0.0000 Min. :0.00000
Class :character 1st Qu.:2011 1st Qu.:8 1st Qu.:28 1st
Qu.:0.0000 1st Qu.:0.00000
Mode :character Median :2011 Median :8 Median :28 Median
:0.0000 Median :0.00000
Mean :2011 Mean :8 Mean :28 Mean
:0.6119 Mean :0.60163
3rd Qu.:2011 3rd Qu.:8 3rd Qu.:28 3rd
Qu.:0.0225 3rd Qu.:0.03953
Max. :2011 Max. :8 Max. :28 Max.
:9.3600 Max. :9.05766
bias type lat lon
city
Min. :-4.75583 Length:236 Min. :33.53 Min. :-84.84
Length:236
1st Qu.: 0.00000 Class :character 1st Qu.:34.37 1st Qu.:-82.71
Class :character
Median : 0.00000 Mode :character Median :35.06 Median :-81.18
Mode :character
Mean :-0.01028 Mean :35.18 Mean :-81.00
3rd Qu.: 0.00000 3rd Qu.:35.99 3rd Qu.:-79.37
Max. : 2.82117 Max. :36.98 Max. :-76.33
state preciptime
Length:236 Length:236
Class :character Class :character
Mode :character Mode :character
> summary(gridmeta)
lon lat xcell ycell
row col
Min. :-86.29 Min. :30.51 Min. :1895112 Min. :-6545105
Min. : 1.00 Min. : 1.0
1st Qu.:-82.38 1st Qu.:33.73 1st Qu.:2184464 1st Qu.:-6330770
1st Qu.: 61.75 1st Qu.: 46.0
Median :-79.88 Median :35.22 Median :2473816 Median :-6114053
Median :122.50 Median : 91.5
Mean :-79.91 Mean :35.26 Mean :2473816 Mean :-6114053
Mean :122.50 Mean : 91.5
3rd Qu.:-77.48 3rd Qu.:36.76 3rd Qu.:2763169 3rd Qu.:-5897337
3rd Qu.:183.25 3rd Qu.:137.0
Max. :-73.16 Max. :40.16 Max. :3052521 Max. :-5683002
Max. :244.00 Max. :182.0
To answer your second question, I'm not quite sure why, but apparently
constraining nmax like that was exactly what it needed, because now it
is producing values.
v.fit = vgm(psill=1.2914,model="Mat",range=14.1611,nugget=0.23,kappa=83.1047)
krige.pred.out =
krige(formula=bias~1,locations=~lon+lat,data=casedata,newdata=gridmeta,model=v.fit)
summary(krige.pred.out)
lon lat var1.pred var1.var
Min. :-86.29 Min. :30.51 Min. :-1.083 Min. :0.253
1st Qu.:-82.38 1st Qu.:33.73 1st Qu.:-0.044 1st Qu.:0.253
Median :-79.88 Median :35.22 Median : 0.000 Median :0.253
Mean :-79.91 Mean :35.26 Mean :-0.051 Mean :0.253
3rd Qu.:-77.48 3rd Qu.:36.76 3rd Qu.: 0.000 3rd Qu.:0.253
Max. :-73.16 Max. :40.16 Max. : 1.252 Max. :0.254
NA's :14925 NA's :31483
Thanks for the help.
Adrienne
On Wed, Oct 31, 2012 at 10:28 AM, ONKELINX, Thierry
<Thierry.ONKELINX at inbo.be> wrote:
> Dear Adrienne,
>
> What is the output of summary(casestudy) and summary(gridmeta)?
>
> What happens if you set nmax to 10?
> krige(formula=bias~1,locations=~lon+lat,data=casedata,newdata=gridmeta ,model=v.fit, nmax = 10)
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
>
> -----Oorspronkelijk bericht-----
> Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Namens Adrienne Wootten
> Verzonden: dinsdag 30 oktober 2012 18:36
> Aan: r-help at r-project.org
> Onderwerp: [R] issues with krige function
>
> Greetings all,
>
> Ran into a strange problem with the krige function from geoR. The problem that I am having is that while the krige function seems to work well, the resulting predicted values are all NAs. Given the size of the datasets I am working with can't attach it, but I can provide snippets of the datasets.
>
>> casedata
> station year month day obs mpe bias type lat lon
> 140 319147 2011 8 28 0.00 0.000000000 0.00000000 COOP 35.48667 -82.96833
> 141 319354 2011 8 28 0.02 0.001305799 -0.01869420 COOP 34.25722 -78.68722
> 142 319357 2011 8 28 0.00 0.045194085 0.04519409 COOP 34.40944 -78.79139
> 143 319440 2011 8 28 6.92 5.530313974 -1.38968603 COOP 35.85278 -77.03056
> 144 319461 2011 8 28 0.98 0.949224103 -0.03077590 COOP 34.14250 -77.87861
> 145 319467 2011 8 28 0.30 1.492852601 1.19285260 COOP 34.32083 -77.92056
> 146 319476 2011 8 28 2.95 3.284362345 0.33436235 COOP 35.69389 -77.94556
> 147 319555 2011 8 28 0.00 0.000000000 0.00000000 COOP 36.13083 -81.22750
> 148 319667 2011 8 28 0.00 0.014472943 0.01447294 COOP 35.85583 -80.36083
> 149 319675 2011 8 28 0.00 0.000000000 0.00000000 COOP 36.13056 -80.54806
>
>> v.fit =
>> vgm(phi=1.2914,model="Mat",range=14.1611,nugget=0.23,kappa=83.1047)
>> krige.pred.out =
>> krige(formula=bias~1,locations=~lon+lat,data=casedata,newdata=gridmeta
>> ,model=v.fit)
> [using ordinary kriging]
>
>> krige.pred.out
> lon lat var1.pred var1.var
> 1 -86.28771 33.91335 NaN NaN
> 2 -86.27388 33.94722 NaN NaN
> 3 -86.26003 33.98111 NaN NaN
> 4 -86.24615 34.01500 NaN NaN
> 5 -86.23225 34.04890 NaN NaN
> 6 -86.21835 34.08280 NaN NaN
> 7 -86.20441 34.11672 NaN NaN
> 8 -86.19045 34.15064 NaN NaN
> 9 -86.17648 34.18457 NaN NaN
> 10 -86.16249 34.21851 NaN NaN
>
>> summary(krige.pred.out)
> lon lat var1.pred var1.var
> Min. :-86.29 Min. :30.51 Min. : NA Min. : NA
> 1st Qu.:-82.38 1st Qu.:33.73 1st Qu.: NA 1st Qu.: NA
> Median :-79.88 Median :35.22 Median : NA Median : NA
> Mean :-79.91 Mean :35.26 Mean :NaN Mean :NaN
> 3rd Qu.:-77.48 3rd Qu.:36.76 3rd Qu.: NA 3rd Qu.: NA
> Max. :-73.16 Max. :40.16 Max. : NA Max. : NA
> NA's :44408 NA's :44408
>
>
> Any ideas are greatly appreciated, I'm not getting any warnings or errors from krige, so this is perplexing to me.
>
> --
> Adrienne Wootten
> Graduate Research Assistant
> State Climate Office of North Carolina
> Department of Marine, Earth and Atmospheric Sciences North Carolina State University
>
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--
Adrienne Wootten
Graduate Research Assistant
State Climate Office of North Carolina
Department of Marine, Earth and Atmospheric Sciences
North Carolina State University
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