help: krigged map do not show colours

classic Classic list List threaded Threaded
9 messages Options
Reply | Threaded
Open this post in threaded view
|

help: krigged map do not show colours

Anand Sookun
Hi

I have kriged my data but the map shows uniform colours - no gradual
contour colour plot on map

code: print(spplot(k40, "var1.pred", asp=1,
col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))

thnaks for any help

Anand Sookun
--
-------------------------------------------------------
*Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
*Director cum Freelance Consultant*
*Soft Sustainable Services (Mauritius)*
*Research and Consultancy*

Website: http://sustain-ability.webs.com/


https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Roman Luštrik
What is the variability of the plotted variable?

Cheers,
Roman

On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun <[hidden email]> wrote:

> Hi
>
> I have kriged my data but the map shows uniform colours - no gradual
> contour colour plot on map
>
> code: print(spplot(k40, "var1.pred", asp=1,
> col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))
>
> thnaks for any help
>
> Anand Sookun
> --
> -------------------------------------------------------
> *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
> *Director cum Freelance Consultant*
> *Soft Sustainable Services (Mauritius)*
> *Research and Consultancy*
>
> Website: http://sustain-ability.webs.com/
>
>
>
> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>



--
In God we trust, all others bring data.

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Anand Sookun
Hi

Thank you Roman for your kind response.

The data is as attached which is part of the whole dataset.

My other problem is that im not able to create an appropriate prediction grid with some data included.

The codes which failed to show colour ramps are

map <- krige(logcarbseq ~ 1, locations = carbon_seq, newdata = map,model = vmf)
str(map)
print(spplot(map, "var1.pred", asp=1, col.regions=bpy.colors(64),main="OK prediction, carbon")) 
print(spplot(map, "var1.var",col.regions=cm.colors(64),asp=1, main="OK prediction variance, carbon"))

I look forward to hopefully get some solutions.

Thanks again and warm regards

Anand

On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik <[hidden email]> wrote:
What is the variability of the plotted variable?

Cheers,
Roman

On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun <[hidden email]> wrote:
Hi

I have kriged my data but the map shows uniform colours - no gradual
contour colour plot on map

code: print(spplot(k40, "var1.pred", asp=1,
col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))

thnaks for any help

Anand Sookun
--
-------------------------------------------------------
*Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
*Director cum Freelance Consultant*
*Soft Sustainable Services (Mauritius)*
*Research and Consultancy*

Website: http://sustain-ability.webs.com/


https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo



--
In God we trust, all others bring data.



--
-------------------------------------------------------
Anand Sookun (MPhil. PhD Candidate, University of Mauritius)
Director cum Freelance Consultant
Soft Sustainable Services (Mauritius)
Research and Consultancy

Website: http://sustain-ability.webs.com/ 


_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

EXAMPLE DATA.csv (844 bytes) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Roman Luštrik
Unfortunately we don't have access to all the variables you use in `krige`
call. Consider making a reproducible example.

Cheers,
Roman


On Mon, Aug 3, 2015 at 5:30 PM, Anand Sookun <[hidden email]> wrote:

> Hi
>
> Thank you Roman for your kind response.
>
> The data is as attached which is part of the whole dataset.
>
> My other problem is that im not able to create an appropriate prediction
> grid with some data included.
>
> The codes which failed to show colour ramps are
>
> map <- krige(logcarbseq ~ 1, locations = carbon_seq, newdata = map,model =
> vmf)
> str(map)
> print(spplot(map, "var1.pred", asp=1, col.regions=bpy.colors(64),main="OK
> prediction, carbon"))
> print(spplot(map, "var1.var",col.regions=cm.colors(64),asp=1, main="OK
> prediction variance, carbon"))
>
> I look forward to hopefully get some solutions.
>
> Thanks again and warm regards
>
> Anand
>
> On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik <[hidden email]>
> wrote:
>
>> What is the variability of the plotted variable?
>>
>> Cheers,
>> Roman
>>
>> On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun <[hidden email]> wrote:
>>
>>> Hi
>>>
>>> I have kriged my data but the map shows uniform colours - no gradual
>>> contour colour plot on map
>>>
>>> code: print(spplot(k40, "var1.pred", asp=1,
>>> col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))
>>>
>>> thnaks for any help
>>>
>>> Anand Sookun
>>> --
>>> -------------------------------------------------------
>>> *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
>>> *Director cum Freelance Consultant*
>>> *Soft Sustainable Services (Mauritius)*
>>> *Research and Consultancy*
>>>
>>> Website: http://sustain-ability.webs.com/
>>>
>>>
>>>
>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>>
>>
>> --
>> In God we trust, all others bring data.
>>
>
>
>
> --
> -------------------------------------------------------
> *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
> *Director cum Freelance Consultant*
> *Soft Sustainable Services (Mauritius)*
> *Research and Consultancy*
>
> Website: http://sustain-ability.webs.com/
>
>
>
> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>
>


--
In God we trust, all others bring data.

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Jon Skoien
In reply to this post by Anand Sookun
Hi,

You have attached some data, but we still dont know exactly what you do
with the data (do you use the logarithm, how many bins, did you project
the data set...?). However, having had a quick look using the LatLong
coordinates (not really recommended), I can see that the variogram from
this data set is not particularly well defined, and it could well be
that you fitted a model with pure nugget effect. In that case you will
get the same prediction everywhere and no color differences.

Have a look at
 > summary(map)
and particularly the summary of var1.pred.
You could also plot the variogram of the data together with your model,
vmf, and see how they fit.

I am not sure what you mean by not being able to create a prediction
grid with data included. Do you mean that you want a grid which exactly
overlays some of the data points? Matching one point should not be
difficult, 2 and 3 should be possible, but you might get some problems
with precision (FAQ 7.31).

Best wishes,
Jon



On 8/3/2015 5:30 PM, Anand Sookun wrote:

> Hi
>
> Thank you Roman for your kind response.
>
> The data is as attached which is part of the whole dataset.
>
> My other problem is that im not able to create an appropriate
> prediction grid with some data included.
>
> The codes which failed to show colour ramps are
>
> map <- krige(logcarbseq ~ 1, locations = carbon_seq, newdata =
> map,model = vmf)
> str(map)
> print(spplot(map, "var1.pred", asp=1,
> col.regions=bpy.colors(64),main="OK prediction, carbon"))
> print(spplot(map, "var1.var",col.regions=cm.colors(64),asp=1, main="OK
> prediction variance, carbon"))
>
> I look forward to hopefully get some solutions.
>
> Thanks again and warm regards
>
> Anand
>
> On Mon, Aug 3, 2015 at 4:09 PM, Roman Lu�trik <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     What is the variability of the plotted variable?
>
>     Cheers,
>     Roman
>
>     On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>         Hi
>
>         I have kriged my data but the map shows uniform colours - no
>         gradual
>         contour colour plot on map
>
>         code: print(spplot(k40, "var1.pred", asp=1,
>         col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))
>
>         thnaks for any help
>
>         Anand Sookun
>         --
>         -------------------------------------------------------
>         *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
>         *Director cum Freelance Consultant*
>         *Soft Sustainable Services (Mauritius)*
>         *Research and Consultancy*
>
>         Website: http://sustain-ability.webs.com/
>
>
>         https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>
>                 [[alternative HTML version deleted]]
>
>         _______________________________________________
>         R-sig-Geo mailing list
>         [hidden email] <mailto:[hidden email]>
>         https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
>
>
>     --
>     In God we trust, all others bring data.
>
>
>
>
> --
> -------------------------------------------------------
> /*Anand Sookun (*//*MPhil. *//*PhD Candidate, University of Mauritius)*/
> /*Director cum Freelance Consultant*/
> /*Soft Sustainable Services (Mauritius)*/
> /*Research and Consultancy*/
>
> Website: http://sustain-ability.webs.com/
>
>
> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>
>
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
--
Jon Olav Sk�ien
Joint Research Centre - European Commission
Institute for Environment and Sustainability (IES)
Climate Risk Management Unit

Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY

[hidden email]
Tel:  +39 0332 789205

Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.


        [[alternative HTML version deleted]]


_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Anand Sookun
Dear Jon and Roman

Thanks for the reply.

Im attaching the code.

You may be right that the variogram may be problematic but it fitted well visually.

I think also that the prediction grid was not well created. I wiould be grateful to have to hints.code how to create a useful grid and also for the spplot or other alternatives

I can send more info if required.

Cheers

Anand

On Tue, Aug 4, 2015 at 1:39 PM, Jon Skoien <[hidden email]> wrote:
Hi,

You have attached some data, but we still dont know exactly what you do with the data (do you use the logarithm, how many bins, did you project the data set...?). However, having had a quick look using the LatLong coordinates (not really recommended), I can see that the variogram from this data set is not particularly well defined, and it could well be that you fitted a model with pure nugget effect. In that case you will get the same prediction everywhere and no color differences.

Have a look at
> summary(map)
and particularly the summary of var1.pred.
You could also plot the variogram of the data together with your model, vmf, and see how they fit.

I am not sure what you mean by not being able to create a prediction grid with data included. Do you mean that you want a grid which exactly overlays some of the data points? Matching one point should not be difficult, 2 and 3 should be possible, but you might get some problems with precision (FAQ 7.31).

Best wishes,
Jon




On 8/3/2015 5:30 PM, Anand Sookun wrote:
Hi

Thank you Roman for your kind response.

The data is as attached which is part of the whole dataset.

My other problem is that im not able to create an appropriate prediction grid with some data included.

The codes which failed to show colour ramps are

map <- krige(logcarbseq ~ 1, locations = carbon_seq, newdata = map,model = vmf)
str(map)
print(spplot(map, "var1.pred", asp=1, col.regions=bpy.colors(64),main="OK prediction, carbon")) 
print(spplot(map, "var1.var",col.regions=cm.colors(64),asp=1, main="OK prediction variance, carbon"))

I look forward to hopefully get some solutions.

Thanks again and warm regards

Anand

On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik <[hidden email]> wrote:
What is the variability of the plotted variable?

Cheers,
Roman

On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun <[hidden email][hidden email]> wrote:
Hi

I have kriged my data but the map shows uniform colours - no gradual
contour colour plot on map

code: print(spplot(k40, "var1.pred", asp=1,
col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))

thnaks for any help

Anand Sookun
--
-------------------------------------------------------
*Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
*Director cum Freelance Consultant*
*Soft Sustainable Services (Mauritius)*
*Research and Consultancy*

Website: http://sustain-ability.webs.com/


https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo



--
In God we trust, all others bring data.



--
-------------------------------------------------------
Anand Sookun (MPhil. PhD Candidate, University of Mauritius)
Director cum Freelance Consultant
Soft Sustainable Services (Mauritius)
Research and Consultancy

Website: http://sustain-ability.webs.com/ 



_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

-- 
Jon Olav Skøien
Joint Research Centre - European Commission
Institute for Environment and Sustainability (IES)
Climate Risk Management Unit

Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY

[hidden email]
Tel:  <a href="tel:%2B39%200332%20789205" value="+390332789205" target="_blank">+39 0332 789205

Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission. 



--
-------------------------------------------------------
Anand Sookun (MPhil. PhD Candidate, University of Mauritius)
Director cum Freelance Consultant
Soft Sustainable Services (Mauritius)
Research and Consultancy

Website: http://sustain-ability.webs.com/ 


_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

To sig geoAug2015.R (2K) Download Attachment
vca_raster.grd (746 bytes) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Jon Skoien
Anand,

I could not open your .grd file in R, I think the .gri file is missing.
However, looking at it in a text editor, and comparing with your
R-script, it seems something went wrong with your projections. Your
.csv-file has LatLong coordinates, but you are setting the projection to
"+proj=utm +zone=40 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84
+towgs84=0,0,0", the same as you seem to have in your prediction raster.
But you need to reproject your observations in this case.

# First set the right projection:
proj4string(carbon_seq) <- CRS("+init=epsg4326") # epsg-code for latlong
# Then transform
carbon_seq = spTransform(carbon_seq, CRS("+proj=utm +zone=40 +south
+datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"))

If you do this, your prediction grid should overlap your observations,
and the colors should reflect your color ramp. What you essentially did
before was to make a prediction thousands of km away from your
observations, and then all values will be the same.

Best wishes,
Jon


On 8/4/2015 12:48 PM, Anand Sookun wrote:

> Dear Jon and Roman
>
> Thanks for the reply.
>
> Im attaching the code.
>
> You may be right that the variogram may be problematic but it fitted
> well visually.
>
> I think also that the prediction grid was not well created. I wiould be
> grateful to have to hints.code how to create a useful grid and also for
> the spplot or other alternatives
>
> I can send more info if required.
>
> Cheers
>
> Anand
>
> On Tue, Aug 4, 2015 at 1:39 PM, Jon Skoien <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi,
>
>     You have attached some data, but we still dont know exactly what you
>     do with the data (do you use the logarithm, how many bins, did you
>     project the data set...?). However, having had a quick look using
>     the LatLong coordinates (not really recommended), I can see that the
>     variogram from this data set is not particularly well defined, and
>     it could well be that you fitted a model with pure nugget effect. In
>     that case you will get the same prediction everywhere and no color
>     differences.
>
>     Have a look at
>      > summary(map)
>     and particularly the summary of var1.pred.
>     You could also plot the variogram of the data together with your
>     model, vmf, and see how they fit.
>
>     I am not sure what you mean by not being able to create a prediction
>     grid with data included. Do you mean that you want a grid which
>     exactly overlays some of the data points? Matching one point should
>     not be difficult, 2 and 3 should be possible, but you might get some
>     problems with precision (FAQ 7.31).
>
>     Best wishes,
>     Jon
>
>
>
>
>     On 8/3/2015 5:30 PM, Anand Sookun wrote:
>>     Hi
>>
>>     Thank you Roman for your kind response.
>>
>>     The data is as attached which is part of the whole dataset.
>>
>>     My other problem is that im not able to create an appropriate
>>     prediction grid with some data included.
>>
>>     The codes which failed to show colour ramps are
>>
>>     map <- krige(logcarbseq ~ 1, locations = carbon_seq, newdata =
>>     map,model = vmf)
>>     str(map)
>>     print(spplot(map, "var1.pred", asp=1,
>>     col.regions=bpy.colors(64),main="OK prediction, carbon"))
>>     print(spplot(map, "var1.var",col.regions=cm.colors(64),asp=1,
>>     main="OK prediction variance, carbon"))
>>
>>     I look forward to hopefully get some solutions.
>>
>>     Thanks again and warm regards
>>
>>     Anand
>>
>>     On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik
>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>
>>         What is the variability of the plotted variable?
>>
>>         Cheers,
>>         Roman
>>
>>         On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun
>>         <<mailto:[hidden email]>[hidden email]
>>         <mailto:[hidden email]>> wrote:
>>
>>             Hi
>>
>>             I have kriged my data but the map shows uniform colours -
>>             no gradual
>>             contour colour plot on map
>>
>>             code: print(spplot(k40, "var1.pred", asp=1,
>>             col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))
>>
>>             thnaks for any help
>>
>>             Anand Sookun
>>             --
>>             -------------------------------------------------------
>>             *Anand Sookun (**MPhil. **PhD Candidate, University of
>>             Mauritius)*
>>             *Director cum Freelance Consultant*
>>             *Soft Sustainable Services (Mauritius)*
>>             *Research and Consultancy*
>>
>>             Website: http://sustain-ability.webs.com/
>>
>>
>>             https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>
>>                     [[alternative HTML version deleted]]
>>
>>             _______________________________________________
>>             R-sig-Geo mailing list
>>             [hidden email] <mailto:[hidden email]>
>>             https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>>
>>
>>         --
>>         In God we trust, all others bring data.
>>
>>
>>
>>
>>     --
>>     -------------------------------------------------------
>>     /*Anand Sookun (*//*MPhil. *//*PhD Candidate, University of
>>     Mauritius)*/
>>     /*Director cum Freelance Consultant*/
>>     /*Soft Sustainable Services (Mauritius)*/
>>     /*Research and Consultancy*/
>>
>>     Website:
>>     <http://sustain-ability.webs.com/>http://sustain-ability.webs.com/
>>
>>
>>     <https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic>https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>
>>
>>
>>     _______________________________________________
>>     R-sig-Geo mailing list
>>     [hidden email] <mailto:[hidden email]>
>>     https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>     --
>     Jon Olav Skøien
>     Joint Research Centre - European Commission
>     Institute for Environment and Sustainability (IES)
>     Climate Risk Management Unit
>
>     Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY
>
>     [hidden email] <mailto:[hidden email]>
>     Tel:+39 0332 789205 <tel:%2B39%200332%20789205>
>
>     Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.
>
>
>
>
> --
> -------------------------------------------------------
> /*Anand Sookun (*//*MPhil. *//*PhD Candidate, University of Mauritius)*/
> /*Director cum Freelance Consultant*/
> /*Soft Sustainable Services (Mauritius)*/
> /*Research and Consultancy*/
>
> Website: http://sustain-ability.webs.com/
>
>
> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>

--
Jon Olav Skøien
Joint Research Centre - European Commission
Institute for Environment and Sustainability (IES)
Climate Risk Management Unit

Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY

[hidden email]
Tel:  +39 0332 789205

Disclaimer: Views expressed in this email are those of the individual
and do not necessarily represent official views of the European Commission.

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Anand Sookun
DearJon

Thnaks. I will try that soon.

Cheers

Anand

On Tue, Aug 4, 2015 at 4:55 PM, Jon Skoien <[hidden email]>
wrote:

> Anand,
>
> I could not open your .grd file in R, I think the .gri file is missing.
> However, looking at it in a text editor, and comparing with your R-script,
> it seems something went wrong with your projections. Your .csv-file has
> LatLong coordinates, but you are setting the projection to "+proj=utm
> +zone=40 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84
> +towgs84=0,0,0", the same as you seem to have in your prediction raster.
> But you need to reproject your observations in this case.
>
> # First set the right projection:
> proj4string(carbon_seq) <- CRS("+init=epsg4326") # epsg-code for latlong
> # Then transform
> carbon_seq = spTransform(carbon_seq, CRS("+proj=utm +zone=40 +south
> +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"))
>
> If you do this, your prediction grid should overlap your observations, and
> the colors should reflect your color ramp. What you essentially did before
> was to make a prediction thousands of km away from your observations, and
> then all values will be the same.
>
> Best wishes,
> Jon
>
>
> On 8/4/2015 12:48 PM, Anand Sookun wrote:
>
>> Dear Jon and Roman
>>
>> Thanks for the reply.
>>
>> Im attaching the code.
>>
>> You may be right that the variogram may be problematic but it fitted
>> well visually.
>>
>> I think also that the prediction grid was not well created. I wiould be
>> grateful to have to hints.code how to create a useful grid and also for
>> the spplot or other alternatives
>>
>> I can send more info if required.
>>
>> Cheers
>>
>> Anand
>>
>> On Tue, Aug 4, 2015 at 1:39 PM, Jon Skoien <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     Hi,
>>
>>     You have attached some data, but we still dont know exactly what you
>>     do with the data (do you use the logarithm, how many bins, did you
>>     project the data set...?). However, having had a quick look using
>>     the LatLong coordinates (not really recommended), I can see that the
>>     variogram from this data set is not particularly well defined, and
>>     it could well be that you fitted a model with pure nugget effect. In
>>     that case you will get the same prediction everywhere and no color
>>     differences.
>>
>>     Have a look at
>>      > summary(map)
>>     and particularly the summary of var1.pred.
>>     You could also plot the variogram of the data together with your
>>     model, vmf, and see how they fit.
>>
>>     I am not sure what you mean by not being able to create a prediction
>>     grid with data included. Do you mean that you want a grid which
>>     exactly overlays some of the data points? Matching one point should
>>     not be difficult, 2 and 3 should be possible, but you might get some
>>     problems with precision (FAQ 7.31).
>>
>>     Best wishes,
>>     Jon
>>
>>
>>
>>
>>     On 8/3/2015 5:30 PM, Anand Sookun wrote:
>>
>>>     Hi
>>>
>>>     Thank you Roman for your kind response.
>>>
>>>     The data is as attached which is part of the whole dataset.
>>>
>>>     My other problem is that im not able to create an appropriate
>>>     prediction grid with some data included.
>>>
>>>     The codes which failed to show colour ramps are
>>>
>>>     map <- krige(logcarbseq ~ 1, locations = carbon_seq, newdata =
>>>     map,model = vmf)
>>>     str(map)
>>>     print(spplot(map, "var1.pred", asp=1,
>>>     col.regions=bpy.colors(64),main="OK prediction, carbon"))
>>>     print(spplot(map, "var1.var",col.regions=cm.colors(64),asp=1,
>>>     main="OK prediction variance, carbon"))
>>>
>>>     I look forward to hopefully get some solutions.
>>>
>>>     Thanks again and warm regards
>>>
>>>     Anand
>>>
>>>     On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik
>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>
>>>         What is the variability of the plotted variable?
>>>
>>>         Cheers,
>>>         Roman
>>>
>>>         On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun
>>>         <<mailto:[hidden email]>[hidden email]
>>>         <mailto:[hidden email]>> wrote:
>>>
>>>             Hi
>>>
>>>             I have kriged my data but the map shows uniform colours -
>>>             no gradual
>>>             contour colour plot on map
>>>
>>>             code: print(spplot(k40, "var1.pred", asp=1,
>>>             col.regions=bpy.colors(64),main="OK prediction, log-ppm Zn"))
>>>
>>>             thnaks for any help
>>>
>>>             Anand Sookun
>>>             --
>>>             -------------------------------------------------------
>>>             *Anand Sookun (**MPhil. **PhD Candidate, University of
>>>             Mauritius)*
>>>             *Director cum Freelance Consultant*
>>>             *Soft Sustainable Services (Mauritius)*
>>>             *Research and Consultancy*
>>>
>>>             Website: http://sustain-ability.webs.com/
>>>
>>>
>>>
>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>>
>>>                     [[alternative HTML version deleted]]
>>>
>>>             _______________________________________________
>>>             R-sig-Geo mailing list
>>>             [hidden email] <mailto:[hidden email]>
>>>             https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>>
>>>
>>>         --
>>>         In God we trust, all others bring data.
>>>
>>>
>>>
>>>
>>>     --
>>>     -------------------------------------------------------
>>>     /*Anand Sookun (*//*MPhil. *//*PhD Candidate, University of
>>>     Mauritius)*/
>>>     /*Director cum Freelance Consultant*/
>>>     /*Soft Sustainable Services (Mauritius)*/
>>>     /*Research and Consultancy*/
>>>
>>>     Website:
>>>     <http://sustain-ability.webs.com/>http://sustain-ability.webs.com/
>>>
>>>
>>>     <
>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>> >
>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>>
>>>
>>>
>>>     _______________________________________________
>>>     R-sig-Geo mailing list
>>>     [hidden email] <mailto:[hidden email]>
>>>     https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>>     --
>>     Jon Olav Skøien
>>     Joint Research Centre - European Commission
>>     Institute for Environment and Sustainability (IES)
>>     Climate Risk Management Unit
>>
>>     Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY
>>
>>     [hidden email] <mailto:[hidden email]>
>>     Tel:+39 0332 789205 <tel:%2B39%200332%20789205>
>>
>>     Disclaimer: Views expressed in this email are those of the individual
>> and do not necessarily represent official views of the European Commission.
>>
>>
>>
>>
>> --
>> -------------------------------------------------------
>> /*Anand Sookun (*//*MPhil. *//*PhD Candidate, University of Mauritius)*/
>> /*Director cum Freelance Consultant*/
>> /*Soft Sustainable Services (Mauritius)*/
>> /*Research and Consultancy*/
>>
>> Website: http://sustain-ability.webs.com/
>>
>>
>>
>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>
>>
> --
> Jon Olav Skøien
> Joint Research Centre - European Commission
> Institute for Environment and Sustainability (IES)
> Climate Risk Management Unit
>
> Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY
>
> [hidden email]
> Tel:  +39 0332 789205
>
> Disclaimer: Views expressed in this email are those of the individual and
> do not necessarily represent official views of the European Commission.
>



--
-------------------------------------------------------
*Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
*Director cum Freelance Consultant*
*Soft Sustainable Services (Mauritius)*
*Research and Consultancy*

Website: http://sustain-ability.webs.com/


https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: help: krigged map do not show colours

Anand Sookun
In reply to this post by Jon Skoien
Dear Jon

I have to thank you so much for solving this issue. I did't notice that
there was a projection and grid problem.

I hope I would be able to move forward with my analysis with R and perhaps
still need your kind and much appreciated help.

Cheers

Anand

On Wed, Aug 5, 2015 at 12:08 PM, Jon Skoien <[hidden email]>
wrote:

> Good.
> For the next function, I think you are trying to use an sp-function
> (gridded) on a raster object. You can convert between these, but not
> necessarily use the same functions. Use
> spgrid = rasterToPoints(YourRaster, spatial = TRUE)
> gridded(spgrid) = TRUE
> if you want to convert your raster layer to a spatial object.
>
> Best wishes,
> Jon
>
>
>
> On 8/5/2015 10:00 AM, Anand Sookun wrote:
>
> Dear John
>
> Thanks again.
> this time it worked but the variogram is not plotting well and some other
> problems croped.
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘gridded’ for signature
> ‘"RasterLayer"
>
> I will try by looking closely at the scripts and be back to you soon
>
> Best Wishes
>
> Anand
>
> On Wed, Aug 5, 2015 at 11:36 AM, Jon Skoien <[hidden email]>
> wrote:
>
>> Dear Anand
>>
>> On 8/5/2015 9:03 AM, Anand Sookun wrote:
>>
>> Dear John
>>
>> Greetings
>>
>> I really appreciate your help. Itried what you proposed but got stuck
>> with the following:
>>
>> > proj4string(carbon_seq) <- CRS("+init=epsg 4326") # epsg-code for
>> latlong
>> Error in CRS("+init=epsg 4326") : no colon in init= string
>>
>> Sorry, there is a : missing, should be
>> CRS("+init=epsg:4326")
>>
>> See if it works better!
>> Jon
>>
>>
>> Also I TRIED AGAIN
>> > proj4string(carbon_seq) <- CRS("+init=epsg4326") # epsg-code for latlong
>> Error in (function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function ‘proj4string<-’ for
>> signature ‘"data.frame", "CRS"
>>
>> I tried with rgdal but got the same eror
>> > require(rgdal)
>> Loading required package: rgdal
>> rgdal: version: 0.8-16, (SVN revision 498)
>> Geospatial Data Abstraction Library extensions to R successfully loaded
>> Loaded GDAL runtime: GDAL 1.10.1, released 2013/08/26
>> Path to GDAL shared files:
>> C:/Users/Anand/Documents/R/win-library/3.0/rgdal/gdal
>> GDAL does not use iconv for recoding strings.
>> Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
>> Path to PROJ.4 shared files:
>> C:/Users/Anand/Documents/R/win-library/3.0/rgdal/proj
>>
>>
>> im attacing the gri file.
>>
>> Thanks for your time.
>>
>> CHEERS
>>
>> ANAND
>>
>> On Tue, Aug 4, 2015 at 4:55 PM, Jon Skoien <
>> <[hidden email]>[hidden email]> wrote:
>>
>>> Anand,
>>>
>>> I could not open your .grd file in R, I think the .gri file is missing.
>>> However, looking at it in a text editor, and comparing with your
>>> R-script, it seems something went wrong with your projections. Your
>>> .csv-file has LatLong coordinates, but you are setting the projection to
>>> "+proj=utm +zone=40 +south +datum=WGS84 +units=m +no_defs +ellps=WGS84
>>> +towgs84=0,0,0", the same as you seem to have in your prediction raster.
>>> But you need to reproject your observations in this case.
>>>
>>> # First set the right projection:
>>> proj4string(carbon_seq) <- CRS("+init=epsg4326") # epsg-code for latlong
>>> # Then transform
>>> carbon_seq = spTransform(carbon_seq, CRS("+proj=utm +zone=40 +south
>>> +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0"))
>>>
>>> If you do this, your prediction grid should overlap your observations,
>>> and the colors should reflect your color ramp. What you essentially did
>>> before was to make a prediction thousands of km away from your
>>> observations, and then all values will be the same.
>>>
>>> Best wishes,
>>> Jon
>>>
>>>
>>> On 8/4/2015 12:48 PM, Anand Sookun wrote:
>>>
>>>> Dear Jon and Roman
>>>>
>>>> Thanks for the reply.
>>>>
>>>> Im attaching the code.
>>>>
>>>> You may be right that the variogram may be problematic but it fitted
>>>> well visually.
>>>>
>>>> I think also that the prediction grid was not well created. I wiould be
>>>> grateful to have to hints.code how to create a useful grid and also for
>>>> the spplot or other alternatives
>>>>
>>>> I can send more info if required.
>>>>
>>>> Cheers
>>>>
>>>> Anand
>>>>
>>>> On Tue, Aug 4, 2015 at 1:39 PM, Jon Skoien <[hidden email]
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>>     Hi,
>>>>
>>>>     You have attached some data, but we still dont know exactly what you
>>>>     do with the data (do you use the logarithm, how many bins, did you
>>>>     project the data set...?). However, having had a quick look using
>>>>     the LatLong coordinates (not really recommended), I can see that the
>>>>     variogram from this data set is not particularly well defined, and
>>>>     it could well be that you fitted a model with pure nugget effect. In
>>>>     that case you will get the same prediction everywhere and no color
>>>>     differences.
>>>>
>>>>     Have a look at
>>>>      > summary(map)
>>>>     and particularly the summary of var1.pred.
>>>>     You could also plot the variogram of the data together with your
>>>>     model, vmf, and see how they fit.
>>>>
>>>>     I am not sure what you mean by not being able to create a prediction
>>>>     grid with data included. Do you mean that you want a grid which
>>>>     exactly overlays some of the data points? Matching one point should
>>>>     not be difficult, 2 and 3 should be possible, but you might get some
>>>>     problems with precision (FAQ 7.31).
>>>>
>>>>     Best wishes,
>>>>     Jon
>>>>
>>>>
>>>>
>>>>
>>>>     On 8/3/2015 5:30 PM, Anand Sookun wrote:
>>>>
>>>>>     Hi
>>>>>
>>>>>     Thank you Roman for your kind response.
>>>>>
>>>>>     The data is as attached which is part of the whole dataset.
>>>>>
>>>>>     My other problem is that im not able to create an appropriate
>>>>>     prediction grid with some data included.
>>>>>
>>>>>     The codes which failed to show colour ramps are
>>>>>
>>>>>     map <- krige(logcarbseq ~ 1, locations = carbon_seq, newdata =
>>>>>     map,model = vmf)
>>>>>     str(map)
>>>>>     print(spplot(map, "var1.pred", asp=1,
>>>>>     col.regions=bpy.colors(64),main="OK prediction, carbon"))
>>>>>     print(spplot(map, "var1.var",col.regions=cm.colors(64),asp=1,
>>>>>     main="OK prediction variance, carbon"))
>>>>>
>>>>>     I look forward to hopefully get some solutions.
>>>>>
>>>>>     Thanks again and warm regards
>>>>>
>>>>>     Anand
>>>>>
>>>>>     On Mon, Aug 3, 2015 at 4:09 PM, Roman Luštrik
>>>>>     <[hidden email] <mailto:[hidden email]>> wrote:
>>>>>
>>>>>         What is the variability of the plotted variable?
>>>>>
>>>>>         Cheers,
>>>>>         Roman
>>>>>
>>>>>         On Sun, Aug 2, 2015 at 11:03 AM, Anand Sookun
>>>>>         <<mailto: <[hidden email]>[hidden email]>
>>>>> <[hidden email]>[hidden email]
>>>>>         <mailto: <[hidden email]>[hidden email]>> wrote:
>>>>>
>>>>>             Hi
>>>>>
>>>>>             I have kriged my data but the map shows uniform colours -
>>>>>             no gradual
>>>>>             contour colour plot on map
>>>>>
>>>>>             code: print(spplot(k40, "var1.pred", asp=1,
>>>>>             col.regions=bpy.colors(64),main="OK prediction, log-ppm
>>>>> Zn"))
>>>>>
>>>>>             thnaks for any help
>>>>>
>>>>>             Anand Sookun
>>>>>             --
>>>>>             -------------------------------------------------------
>>>>>             *Anand Sookun (**MPhil. **PhD Candidate, University of
>>>>>             Mauritius)*
>>>>>             *Director cum Freelance Consultant*
>>>>>             *Soft Sustainable Services (Mauritius)*
>>>>>             *Research and Consultancy*
>>>>>
>>>>>             Website: <http://sustain-ability.webs.com/>
>>>>> http://sustain-ability.webs.com/
>>>>>
>>>>>
>>>>>
>>>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>>>>
>>>>>                     [[alternative HTML version deleted]]
>>>>>
>>>>>             _______________________________________________
>>>>>             R-sig-Geo mailing list
>>>>>             <[hidden email]>[hidden email] <mailto:
>>>>> [hidden email]>
>>>>>             https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>         --
>>>>>         In God we trust, all others bring data.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>     --
>>>>>     -------------------------------------------------------
>>>>>     /*Anand Sookun (*//*MPhil. *//*PhD Candidate, University of
>>>>>     Mauritius)*/
>>>>>     /*Director cum Freelance Consultant*/
>>>>>     /*Soft Sustainable Services (Mauritius)*/
>>>>>     /*Research and Consultancy*/
>>>>>
>>>>>     Website:
>>>>>     <http://sustain-ability.webs.com/>
>>>>> <http://sustain-ability.webs.com/>http://sustain-ability.webs.com/
>>>>>
>>>>>
>>>>>     <
>>>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>>>> >
>>>>> <https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic>
>>>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>>>>
>>>>>
>>>>>
>>>>>     _______________________________________________
>>>>>     R-sig-Geo mailing list
>>>>>     [hidden email] <mailto:[hidden email]>
>>>>>     https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>
>>>>     --
>>>>     Jon Olav Skøien
>>>>     Joint Research Centre - European Commission
>>>>     Institute for Environment and Sustainability (IES)
>>>>     Climate Risk Management Unit
>>>>
>>>>     Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY
>>>>
>>>>     [hidden email] <mailto:[hidden email]>
>>>>     Tel:+39 0332 789205 <%2B39%200332%20789205>
>>>> <tel:%2B39%200332%20789205> <%2B39%200332%20789205>
>>>>
>>>>     Disclaimer: Views expressed in this email are those of the
>>>> individual and do not necessarily represent official views of the European
>>>> Commission.
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------------------------------------
>>>> /*Anand Sookun (*//*MPhil. *//*PhD Candidate, University of Mauritius)*/
>>>> /*Director cum Freelance Consultant*/
>>>> /*Soft Sustainable Services (Mauritius)*/
>>>> /*Research and Consultancy*/
>>>>
>>>> Website: http://sustain-ability.webs.com/
>>>>
>>>>
>>>>
>>>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>>>
>>>>
>>> --
>>> Jon Olav Skøien
>>> Joint Research Centre - European Commission
>>> Institute for Environment and Sustainability (IES)
>>> Climate Risk Management Unit
>>>
>>> Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY
>>>
>>> [hidden email]
>>> Tel:  +39 0332 789205 <%2B39%200332%20789205>
>>>
>>> Disclaimer: Views expressed in this email are those of the individual
>>> and do not necessarily represent official views of the European Commission.
>>>
>>
>>
>>
>> --
>> -------------------------------------------------------
>> *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
>> *Director cum Freelance Consultant*
>> *Soft Sustainable Services (Mauritius)*
>> *Research and Consultancy*
>>
>> Website:  <http://sustain-ability.webs.com/>
>> http://sustain-ability.webs.com/
>>
>>
>>
>> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>>
>>
>> --
>> Jon Olav Skøien
>> Joint Research Centre - European Commission
>> Institute for Environment and Sustainability (IES)
>> Climate Risk Management Unit
>>
>> Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY
>> [hidden email]
>> Tel:  +39 0332 789205
>>
>> Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.
>>
>>
>
>
> --
> -------------------------------------------------------
> *Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
> *Director cum Freelance Consultant*
> *Soft Sustainable Services (Mauritius)*
> *Research and Consultancy*
>
> Website:  <http://sustain-ability.webs.com/>
> http://sustain-ability.webs.com/
>
>
>
> <https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic>
> https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic
>
>
> --
> Jon Olav Skøien
> Joint Research Centre - European Commission
> Institute for Environment and Sustainability (IES)
> Climate Risk Management Unit
>
> Via Fermi 2749, TP 100-01,  I-21027 Ispra (VA), ITALY
> [hidden email]
> Tel:  +39 0332 789205
>
> Disclaimer: Views expressed in this email are those of the individual and do not necessarily represent official views of the European Commission.
>
>


--
-------------------------------------------------------
*Anand Sookun (**MPhil. **PhD Candidate, University of Mauritius)*
*Director cum Freelance Consultant*
*Soft Sustainable Services (Mauritius)*
*Research and Consultancy*

Website: http://sustain-ability.webs.com/


https://www.linkedin.com/profile/view?id=161468467&trk=nav_responsive_tab_profile_pic

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo