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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Thierry,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks for the suggestions. I hadn’t
tried that previously, but no it doesn’t make any difference
unfortunately.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I removed the separate predpoints dataframe
from it and tried using the x and y values from the covars for the prediction,
but got the following:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>> kcontrol<-krige.control(obj.m=mlx2,
type.krige="ok", trend.d=~otuboidist + lstphan,
trend.l=~covars$otuboidist + covars$lstphan) <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>> krige<-krige.conv(nicola, loc=covars,
krige=kcontrol)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>krige.conv: model with mean defined by covariates provided
by the user<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>krige.conv: Kriging performed using global neighbourhood <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Warning message:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>locations provided with a matrix or data-frame with more
than 2 columns. Only the first two columns used as coordinates in:
.check.locations(locations) <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>> image(krige, col=gray(seq(1, 0.2, l=100)))<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Error in image.kriging(krige, col = gray(seq(1, 0.2, l =
100))) : <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> locations must be
a matrix or data-frame with two columns<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Removing the prediction locations from the
covariate dataframe made no difference.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Also, changing the covariate names didn’t
make any difference – I still got the odd prediction results.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I’m thinking perhaps it’s my
prediction grid…I created it in Arc as a shape file with points for each
prediction locations, and then saved the points as a .csv file. Perhaps
the problem has something to do with this? But I’m really a total
novice to both geostatistics and to R, so I could be very wrong!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Nicola<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=3 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> ONKELINX,
Thierry [mailto:Thierry.ONKELINX@inbo.be] <br>
<b><span style='font-weight:bold'>Sent:</span></b> 29 August 2008 09:52<br>
<b><span style='font-weight:bold'>To:</span></b> Nicola Batchelor;
r-sig-geo@stat.math.ethz.ch<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [R-sig-Geo]
Prediction locations for kriging in geoR</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>Dear Nicola,</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>I think that since the
covars contains the locations of the predpoints you don't need two
dataframes. Futhermore make sure that the names of the covars are identical
(including capitalisation).</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>mlx2<-likfit(nicola, cov.model="mat", kap=0.5, ini=c(0.6,
20), nug=0.3, trend=~OTUBOIDIST + LSTPHAN) <br>
kcontrol<-krige.control(obj.m=mlx2, type.krige="ok",
trend.d=~OTUBOIDIST + LSTPHAN, trend.l=~OTUBOIDIST + LSTPHAN) <br>
krige<-krige.conv(nicola, loc=covars, krige=kcontrol)<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>Does that work?</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>HTH,</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>Thierry</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
10.0pt'>----------------------------------------------------------------------------<br>
ir. Thierry Onkelinx<br>
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest<br>
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology
and quality assurance<br>
Gaverstraat 4<br>
9500 Geraardsbergen<br>
Belgium<br>
tel. + 32 54/436 185<br>
Thierry.Onkelinx@inbo.be<br>
www.inbo.be<br>
<br>
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.<br>
~ Sir Ronald Aylmer Fisher<br>
<br>
The plural of anecdote is not data.<br>
~ Roger Brinner<br>
<br>
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.<br>
~ John Tukey</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span lang=NL style='font-size:12.0pt'>
<hr size=3 width="100%" align=center tabIndex=-1>
</span></font></div>
<p class=MsoNormal style='margin-bottom:12.0pt'><b><font size=2 face=Tahoma><span
lang=NL style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>Van:</span></font></b><font
size=2 face=Tahoma><span lang=NL style='font-size:10.0pt;font-family:Tahoma'>
r-sig-geo-bounces@stat.math.ethz.ch
[mailto:r-sig-geo-bounces@stat.math.ethz.ch] <b><span style='font-weight:bold'>Namens
</span></b>Nicola Batchelor<br>
<b><span style='font-weight:bold'>Verzonden:</span></b> vrijdag 29 augustus
2008 10:19<br>
<b><span style='font-weight:bold'>Aan:</span></b> r-sig-geo@stat.math.ethz.ch<br>
<b><span style='font-weight:bold'>Onderwerp:</span></b> [R-sig-Geo] Prediction
locations for kriging in geoR</span></font><span lang=NL><o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>Hi, <br>
<br>
Im using geoR and I'm trying to do some predictions, based on an external
trend, using ordinary kriging.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>However, I seem to be getting some strange results
from my kriging, which I think must have something to do with a problem with my
prediction points. <br>
<br>
I have my geodata object (called nicola), my prediction points (predpoints,
imported from a csv containing only the x and y coordinated of the prediction
locations) and my covariate data at each of the prediction points (covars,
imported from a csv containing the x and y coordinates of the prediction
locations, plus the values of the two covariates I want to use at each of the
prediction locations). <br>
<br>
>predpoints<-read.csv(file="C:\\Documents and Settings\\s9901315\\My
<br>
+ Documents\\Uni\\Data\\Work\\Case control study\\Full study area\\R\\Files for
analysis\\Prediction <br>
+ points\\predpoints.csv", header=FALSE, sep=",") <br>
<br>
>covars<-read.csv(file="C:\\Documents and Settings\\s9901315\\My <br>
+ Documents\\Uni\\Data\\Work\\Case control study\\Full study area\\R\\Files for
analysis\\Covariate <br>
+ data\\covars.csv", header=TRUE, sep=",") <br>
<br>
The final model is defined using "OTUBOIDIST" and "LSTPHAN"
as external covariates: <br>
<br>
>mlx2<-likfit(nicola, cov.model="mat", kap=0.5, ini=c(0.6, 20),
nug=0.3, trend=~OTUBOIDIST + <br>
+ LSTPHAN) <br>
<br>
and then I carry out the kriging using the model "mlx2", prediction
points "predpoints", and covariate data "covars" : <br>
<br>
>kcontrol<-krige.control(obj.m=mlx2, type.krige="ok",
trend.d=~OTUBOIDIST + LSTPHAN, <br>
+ trend.l=~covars$otuboidist + covars$lstphan) <br>
<br>
>krige<-krige.conv(nicola, loc=predpoints, krige=kcontrol) <br>
<br>
Then I view it using the image function: <br>
<br>
>image(krige, col=gray(seq(1, 0.2, l=100))) <br>
<br>
The resulting image is clearly wrong with a regular stepped line appearing
diagonally across the image, and the predicted values do not coincide with the
actual observed data at all. I've included the predicted data image, as
well as the predicted image overlaid with the data points.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>Can anyone give me any pointers of why this may be
going wrong? I've tried the same thing many times having changed
everything I can think of that might be causing the problem. <br>
<br>
Thanks in advance, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'>Nicola<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span lang=EN-GB
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span lang=EN-GB style='font-size:
10.0pt;font-family:Arial'><img width=483 height=429 id="_x0000_i1025"
src="cid:image001.jpg@01C909C5.BEB2DC90"><img width=477 height=433
id="_x0000_i1031" src="cid:image002.jpg@01C909C5.BEB2DC90"><o:p></o:p></span></font></p>
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