[R-sig-Geo] Moving-window sum in a matrix

[Edzer J. Pebesma]

Stephane, have you tried how well this scales to, say, 1000x1000 
matrices? Indeed, most basic raster GIS functionality is not available 
in R packages, and would be welcome. R code is efficient for small
problems, but for cases like this scales badly as Marius noted.

We are actually working on an interface from R to the functionality of 
PCRaster (http://pcraster.geog.uu.nl -- yet another raster GIS), and 
expect to have this working within a few months. PCRaster is not open 
source, so it is unlikely to become a CRAN package straight away, but 
still it may fill a need.

This all depends on availability of sp, the long awaited package with S 
classes for spatial point, line, grid, arc/node and polygon data. We're 
working very hard on this, and most likely will announce a beta in 
January. I expect a PCRasteR package to follow that soon.
--
Edzer

Stephane DRAY wrote:
> Hello,
> I think that you could do it using spdep package. I suppose that, if you:
> - construct a neighborhoord object (nb class). You can define a distance 
> based neighborhood (using dnearneigh) as it seems that your definition 
> is similar to say i and j neighbors if 
> 0<dij<sqrt(cellsize^2+(2*cellsize)^2)
> - then transform the nb to listw with nb2listw with style="B"
> - then use lag.listw to sompute the sum
> 
> an example:
>  > myvalues=rbinom(100,size=1,prob=0.5)
>  > xy=expand.grid(1:10,1:10)
>  > dnn1=dnearneigh(as.matrix(xy),0,sqrt(1+4))
>  > plot(dnn1,as.matrix(xy))
>  > nb2listw(dnn1,style="B")
>  > lw1=nb2listw(dnn1,style="B")
>  > sum.neigh=lag.listw(lw1,myvalues)
>  > sum.neigh
>   [1]  3  6  4  5  7  5  4  4  3  3  6  8  6  7  9  8  6  8  6  4  5  9 
> 10 11 10  7  8  9  7  5
>  [31]  7 10 14 11 10  8  8  9  8  5  8 12 11 10 11 12 10 12 11  7  9 11 
> 12  9 13 11 10 12 12  9
>  [61]  6 11 12 13 10 12 10 13  9  7  6  9 12 10 12 10 13 12  9  5  6  8  
> 8 10 10 11  8  9  7  5
>  [91]  4  6  7  6  9  7  6  4  5  3
> 
> Roger could confirm that it is correct !
> 
> 
> 
> At 10:05 16/12/2004, Marius Gilbert wrote:
> 
>> Dear colleagues,
>>
>> I have a 500 by 500 matrix with presence or absence value in each cell as
>> an input matrix. I am trying to create an output matrix having in each
>> cell the sum of the values from neigbouring cells in the input matrix
>> according to a moving-window defined as:
>>
>> 0 1 1 1 0
>> 1 1 1 1 1
>> 1 1 0 1 1
>> 1 1 1 1 1
>> 0 1 1 1 0
>>
>> where the output cell receiving the values is located in the center. I
>> have written a function that loop over the cells of the output matrix, 
>> and
>> sum up the values from these neigbouring cells. It works, but it is 
>> fairly
>> slow, and hangs if I try it over a larger matrix. Given that this is a
>> rather basic function available in most raster GIS packages (IDRISI 
>> and AV
>> Spatial Analyst) and running fairly quickly, I wondered whether anyone 
>> had
>> previously come accross a similar function in an existing R-package.
>>
>> Any helps  or pointer would be appreciated,
>>
>> Many thanks in advance,
>>
>> Marius
>>
>> _______________________________________________
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> 
> 
> Stéphane DRAY
> -------------------------------------------------------------------------------------------------- 
> 
> Département des Sciences Biologiques
> Université de Montréal, C.P. 6128, succursale centre-ville
> Montréal, Québec H3C 3J7, Canada
> 
> Tel : (514) 343-6111 poste 1233         Fax : (514) 343-2293
> E-mail : stephane.dray at umontreal.ca
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