[R-sig-Geo] [DKIM] Re: FW: Spatial sampling design using information more than spatial coordinates [SEC=UNCLASSIFIED]

Fri Apr 10 12:09:12 CEST 2015

Jin,

When it comes to stratification prior to any model building (hence no 
prior predictions) I think that a robust way to stratify an area would 
be to use a combination of PCA and unsupervised fuzzy k-means. Here is 
an example:

R> library(GSIF)
R> library(plotKML)
R> library(sp)
R> data(eberg_grid)
R> gridded(eberg_grid) <- ~x+y
R> proj4string(eberg_grid) <- CRS("+init=epsg:31467")
R> formulaString <- ~ PRMGEO6+DEMSRT6+TWISRT6+TIRAST6
R> eberg_spc <- spc(eberg_grid, formulaString)
Converting PRMGEO6 to indicators...
Converting covariates to principal components...
R> kmeans.eberg <- kmeans(eberg_spc at predicted@data, 4)
R> eberg_grid$cluster.4 <- as.factor(kmeans.eberg$cluster)
R> spplot(eberg_grid["cluster.4"], col.regions=rainbow(4))

I had problems following the procedure you described (a combination of 
geographical clustering first, then sampling in feature space). Maybe 
you do only need to use the clhs 
(http://www.inside-r.org/packages/cran/clhs/docs) or lhs package because 
this is a standard statistical method when it comes to sampling in 
feature space? It all depends on what is the purpose of sampling - 
validation, model building (maximum representation)...

HTH

Tom #1

On 9-4-2015 3:49, Jin.Li at ga.gov.au wrote:
> Hi Tom 2  :-),
>
> To be specific,  we need to do the spatial stratification first and need
> to stratify the survey area into n equal-area strata. The function
> stratify with equalArea in spcosa meets this need well.
>
> And then within each stratum, we need to do further stratification based
> on a raster layer of 'elevation' that is a continuous layer and needs to
> be converted into 3 zones. We need to sample m samples within each
> stratum and these samples need to be evenly distributed within each
> zone. That is we need to use the area of each zone as a weight to decide
> how many samples should be allocated to each zone. And then do randomly
> sampling within each zone.
>
> A further challenge is that they plan to sample 1 to 4 samples a day
> during 25 days, so we need to provide four designs with 25, 50, 75 and
> 100 samples respectively. The samples of the design with smaller sample
> size need to be nested in the samples of the design with larger sample
> size for operational reasons as the survey needs to meet other tasks and
> also to accommodate weather conditions at sea. Now you know the
> 'elevation' is bathymetry that is the depth of water. We plan to let n =
> 25, and m = 1 to 4. But it is hard to stratify if a stratum contains 3
> zones and m <3.
>
> Hope this clarify things a bit. Any further suggestions are appreciated!
>
> Jin
>
> -----Original Message-----
> From: R-sig-Geo [mailto:r-sig-geo-bounces at r-project.org] On Behalf Of
> Tom Philippi
> Sent: Thursday, 9 April 2015 9:32 AM
> To: Tomislav Hengl
> Cc: r-sig-geo
> Subject: [DKIM] Re: [R-sig-Geo] FW: Spatial sampling design using
> information more than spatial coordinates [SEC=UNCLASSIFIED]
>
> Jin--
>
> Could you provide more information on what the needs of your client are
> that cannot be handled by either stratification or unequal probability
> based on your one or more covariates in spsurvey?  Also, is your sample
> frame points, polygons, or raster?  I assume your covariates are raster
> (e.g., DEM for elevation) and polygons (most soil maps)?
>
> Tom 2
>
> On Wed, Apr 8, 2015 at 6:39 AM, Tomislav Hengl
> <hengl at spatial-analyst.net <mailto:hengl at spatial-analyst.net>>
>
> wrote:
>
>  >
>
>  > The "clhs" package (http://cran.r-project.org/web/packages/clhs/) has
>
>  > some functionality for latin-hypercube sampling hence it is suitable
>
>  > for your case. Here are some code examples: http://gsif.isric.org/doku.
>
>  > php?id=wiki:tutorial_eberg#testing_the_feature_space_coverage
>
>  >
>
>  > I have also recently (experimentally) implemented a function to test
>
>  > 'efficiency of any sampling plan' which looks at both geographical
>
>  > space and feature space representation: http://gsif.r-forge.r-project.
>
>  > org/spsample.prob.html
>
>  > If you discover a bug or some 'strange behavior', please let me know.
>
>  >
>
>  > HTH,
>
>  >
>
>  > T. (Tom) Hengl
>
>  > Researcher @ ISRIC - World Soil Information Team member Africa Soil
>
>  > Information Services http://africasoils.net
>
>  > Url: http://www.wageningenur.nl/en/Persons/dr.-T-Tom-Hengl.htm
>
>  > Network: http://profiles.google.com/tom.hengl
>
>  > Publications: http://scholar.google.com/citations?user=2oYU7S8AAAAJ
>
>  >
>
>  >
>
>  >
>
>  > On 8-4-2015 2:24, Jin.Li at ga.gov.au <mailto:Jin.Li at ga.gov.au> wrote:
>
>  >
>
>  >> Sorry for not ccing to the list!
>
>  >>
>
>  >> -----Original Message-----
>
>  >> From: Li Jin
>
>  >> Sent: Tuesday, 7 April 2015 9:36 AM
>
>  >> To: 'Roger.Bivand at nhh.no'
>
>  >> Subject: RE: [R-sig-Geo] Spatial sampling design using information
>
>  >> more than spatial coordinates [SEC=UNCLASSIFIED]
>
>  >>
>
>  >> Thanks a lot, Roger! Yes, we have looked at spsurvey and it does not
>
>  >> meet the needs of our client.
>
>  >> Kind regards,
>
>  >> Jin
>
>  >>
>
>  >> -----Original Message-----
>
>  >> From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
>
>  >> Sent: Friday, 3 April 2015 2:06 AM
>
>  >> To: Li Jin
>
>  >> Cc: r-sig-geo at r-project.org <mailto:r-sig-geo at r-project.org>
>
>  >> Subject: Re: [R-sig-Geo] Spatial sampling design using information
>
>  >> more than spatial coordinates [SEC=UNCLASSIFIED]
>
>  >>
>
>  >> On Thu, 2 Apr 2015, Jin.Li at ga.gov.au <mailto:Jin.Li at ga.gov.au> wrote:
>
>  >>
>
>  >>  Hi All,
>
>  >>>
>
>  >>> I need to consider both spatial information and another variable (e.g.
>
>  >>> elevation, soil type) in a sampling design. It seems the available
>
>  >>> libraries (e.g. sp and spcosa) in R for spatial sampling design are
>
>  >>> unable to handle it. Please correct me if I am wrong. Before I start
>
>  >>> to develop my own function for it, I would like to confirm if I have
>
>  >>> missed some other functions that are available for it in R.  Any
>
>  >>> suggestions and advice? Thanks in advance!
>
>  >>>
>
>  >>
>
>  >> Have you looked at spsurvey? It may not provide what you need, but
>
>  >> checking it would probably help you see whether there is anything
>
>  >> meeting your needs. Otherwise you might need to stratify first on
> your covariates.
>
>  >>
>
>  >> Roger
>
>  >>
>
>  >>
>
>  >>> Regards,
>
>  >>> Jin
>
>  >>>
>
>  >>> Jin Li, PhD
>
>  >>> Spatial Modeller/Computational Statistician  |  National Earth and
>
>  >>> Marine Observations Group Environmental Geoscience Division  |
>
>  >>> GEOSCIENCE AUSTRALIA ______________________________
>
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>
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> <mailto:Jin.Li at ga.gov.au%3cmailto:Jin.Li at ga.gov.au>>    Web:
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>
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>
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>
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>  >> --
>
>  >> Roger Bivand
>
>  >> Department of Economics, Norwegian School of Economics, Helleveien
>
>  >> 30,
>
>  >> N-5045 Bergen, Norway.
>
>  >> voice: +47 55 95 93 55; fax +47 55 95 91 00
>
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>
>  >>
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