[R-sig-Geo] variogram question

[Paul Hiemstra]

Hi,

The package Edzer was talking about, automap, can be downloaded from 
http://intamap.geo.uu.nl/~paul/Downloads.html. It makes a few practical, 
somewhat arbitrary assumptions about initial starting values.

- initial nugget is lowest semivariance found in the sample variogram
- initial sill is the mean of the maximum and the median semivariance 
value in the sample variogram
- initial range is 0.1 times the diameter of the area.

These settings work for me and, no garantee that it will work on all 
data. After installing the package try demo(automap) for a demonstration.

hth and cheers,
Paul

Edzer Pebesma schreef:
> In general: no, in special cases: yes.
>
> Fitting variograms involves non-linear regression for most models 
> (Sph, Exp, Gau, ...) for the range parameter, so you need starting 
> values. Given the initial range, linear regression is sufficient to 
> find the nugget/sill component(s), as they are linear. In principle, 
> gstat could be made simpler in that respect, I'd say.
>
> For an initial range, you could use some heuristics (20% of the 
> longest distance in your data?), but it is often not so hard to think 
> of cases where this would fail.
>
> Another issue is automatic values for the width and cutoff.
>
> You could have a look at package automap, by Paul Hiemstra, which 
> tries to do some of these heuristics--good or bad, who will tell.
> -- 
> Edzer
>
> Wesley Roberts wrote:
>> Dear r-sig-geo users,
>>
>> I am currently analyzing some Lidar data we have collected over our 
>> study area. I am interested in identifying the range of the 
>> semi-variogram as this value will determine the width of 
>> pseudo-flight lines I intend to use to sample the lidar data. Our 
>> point density is upwards of 5 points per square meter captured over 
>> even-aged managed Eucalyptus plantations with an espacement of 2 
>> meters between trees and 3 meters between rows.
>> I have imported an x,y,z data set containing canopy height and 
>> coordinates and successfully run the experimental variogram using the 
>> "variogram" module in gstat.
>> cpy.pts2 <- variogram(dbl_5 ~ 1, cutoff=50, width=2, D)
>>
>> I have also managed to fit several models using the
>> cpy.pts2.fit <- fit.variogram(cpy.pts2, model = vgm(2, "Sph", 4, 5))
>>
>> command as suggested by the gstat manual. I would like to fit the 
>> various models "Sph, Exp..." etc without having to specify the nugget 
>> psill and range. Essentially I would like an objective method to 
>> measure and record these values as I will be running several hundred 
>> variograms. Is it possible to perform this type of analysis using gstat?
>>
>> Many thanks for all your help and suggestions
>> Wesley
>>
>> Wesley Roberts MSc.
>> Researcher
>> Earth Observation (Ecosystems)
>> Natural Resources and the Environment
>> CSIR
>> Tel: +27 (21) 888-2490
>> Fax: +27 (21) 888-2490
>>
>> "To know the road ahead, ask those coming back."
>> - Chinese proverb
>>
>>   
>


-- 
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