[R-sig-Geo] Spatial and multilevel model with kriging/interpolation in R

Thu Sep 25 11:11:31 CEST 2014

Hi

As Thierry points out INLA is certainly one way to go. Very powerful. For some inspiration see the tutorials and example on the INLA web site. Perhaps the geostatinla package for R (http://pbrown.ca/geostatsp/document-rev.pdf) can be of use for you. Also the section on geoadditive models in http://www.rni.helsinki.fi/~jmh/mrf08/R-INLA.pdf may give you some ideas.

The nlme package for R can fit the same kind of models, see e.g. http://www.ats.ucla.edu/stat/r/faq/spatial_regression.htm. 

Yours sincerely / Med venlig hilsen

Frede Aakmann Tøgersen
Specialist, M.Sc., Ph.D.
Plant Performance & Modeling

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> -----Original Message-----
> From: r-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-
> project.org] On Behalf Of ONKELINX, Thierry
> Sent: 25. september 2014 09:27
> To: Justice Moses K. Aheto; r-sig-geo at r-project.org
> Subject: Re: [R-sig-Geo] Spatial and multilevel model with
> kriging/interpolation in R
> 
> Have a look at the INLA package (www.r-inla.org)
> 
> Best regards,
> 
> 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-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-
> project.org] Namens Justice Moses K. Aheto
> Verzonden: donderdag 25 september 2014 4:25
> Aan: r-sig-geo at r-project.org
> Onderwerp: [R-sig-Geo] Spatial and multilevel model with
> kriging/interpolation in R
> 
> Dear All,
> Please, I wish to analyse a spatial data in R through multilevel approach with
> my main primary objective been to interpolate for unsampled locations in my
> study region. Children in my data set are nested within households in the
> study locations and my multilevel model (without spatial) showed significant
> household random effects hence my choice to employ spatial analysis with
> multilevel approach.
> The need to include household random effects in my spatial model makes it a
> bit difficult for me to implement in R unlike the standard geostatical analysis.
> I have 'SpatialPointsDataFrame' containing my geographical coordinates
> (longitude and latitude) as well as my response and covariates.
> The spatial mixed effects model I wish to fit and interpolate is: Yij(t) = Xij(t)β
> +hj+S(t)+Ɛij           (1)
> where
> i=individual child, j=household, X(t)= spatial referenced non-random
> covariates, S(t)= spatially correlated stationary Gaussian process.
> Ɛij =nugget effect/measurement error, Yij(t) = response of child i in
> household j at location t and is a continuous variable, hj =household level
> random effects and β=regression coefficients (spatial trend parameter).
> Specifically, S(t)~N(0,σ2H11(ɸ) ), where σ2  is the variance (partial sill),
> H11(ɸ) is the correlation matrix based on valid correlation function h(u; ɸ),
> where u is the distance between locations and ɸ is the correlation parameter
> (range).
> hj~N(0, σ2h), where σ2h is the household level variance Ɛij~N(0,τ2), where
> τ2 is the nugget effect/measurement error.
> 
> I am trying to achieve the above task through geostatistical analysis but other
> methods which can be implemented in R are also welcomed.
> 
> 
> Please, could somebody help me with some papers in the literature, existing
> packages in R which are related to my problem as well as providing me with R
> codes to implement this assuming someone has already done this kind of
> multilevel spatial regression and interpolation in R or other packages.
> 
> Many thanks for your help in advance.
> 
> 
> Kind regards
> 
> *****************************************
> Justice Moses K. Aheto
> PhD Candidate in Medicine (United Kingdom) MSc Medical Statistics (United
> Kingdom) BSc Statistics (Ghana) HND Statistics (Ghana)
> 
> Chief Executive Officer
> Statistics and Analytics Consultancy Services Ltd.
> 
> Skype: jascall12
> Mobile:
>  +447417589148.
>         [[alternative HTML version deleted]]
> 
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