[R-sig-Geo] How to handle NA-values in raster-based Geary´s C test?

[Roger Bivand]

On Thu, 12 Jul 2012, Kerstin Traut wrote:

> Zitat von Roger Bivand <Roger.Bivand at nhh.no>:
>
>> On Thu, 12 Jul 2012, Kerstin Traut wrote:
>> 
>>> Hi,
>>> 
>>> I have a question on testing spatial autocorrelation on raster data 
>>> including NA-values. In particular, I like to calculate Moran´s I and 
>>> Geary´s C indices by using inverse distance weighting matrices.
>>> Calculating Moran´s I with moran.test works fine, because the function 
>>> contains the option "na.action=na.pass". Unfortunately, the function 
>>> geary.test does not contain this option. The problem is that geary.test 
>>> needs an nb argument for which I cannot perform for example 
>>> nb<-ifelse(value, nb, NA), because it would change the nb-format to a 
>>> list-format.
>>> Is there a way to ignore NA-values in geary.test? Or how can I set NA 
>>> values in a neigbors (nb) list?
>> 
>> The simple answer is to subset the variable of interest and the nb object 
>> to omit NA observations (which is what moran.test does internally). 
>> Alternatively, you could contribute a patch to geary.test(), if you like.
>> 
>> Hope this helps,
>> 
>> Roger
>
> Thanks for your answer. Unfortunately, I think that subsetting is in my case 
> not the right solution, because I need to define the amount of neighbors in 
> cell2nb on the basis of a rectangular extent (e.g. 50 x 50 neighbors). 
> Subsetting this extent by deleting NA-values would destroy the nb list format 
> required by geary.test.
> Is there any solution for subsetting an nb list without destroying the nb 
> format?

Yes, there are subset methods for nb and listw objects. To ensure data 
integrity, use dnearneigh() instead of cell2nb(), and use a 
SpatialPointsDataFrame to hold your data. In that way, you make sure that 
the subset condition is applied to the same observations.

Roger

>
> Kind regards,
> Kerstin
>
>
>>> Thank you very much,
>>> Kerstin
>>> 
>>> ---
>>> 
>>> file<-raster(test.tif")
>>> mask<-extent(file, 1, 50, 1, 50)
>>> subset<-crop(file,mask,test.tif", overwrite=TRUE)
>>> value <- as.matrix(subset)
>>> 
>>> # Creation of a list of integer vectors giving the region id numbers for 
>>> the neighbors within the grid extent
>>> nb <- cell2nb(50, 50, type="queen", torus=TRUE)
>>> 
>>> # Calculation of the distances along the links in the neighbous list
>>> dist <- nbdists(nb, coordinates(subset), longlat=TRUE)
>>> 
>>> # Converting the distances to inverse distance values
>>> inv.dist <- lapply(dist, function (x) 1/(x*100))
>>> 
>>> # Supplementing the neighbors list with spatial weights for a coding 
>>> scheme
>>> nb.idw <- nb2listw(nb, glist=inv.dist, style="W")
>>> summary(unlist(nb.idw$weights))
>>> 
>>> # Moran's test (two-sided)
>>> moran.global <- moran.test(value, listw=nb.idw, zero.policy = TRUE, 
>>> na.action=na.pass, alternative="two.sided")
>>> moran.global
>>> 
>>> # Geary's test (two-sided)
>>> geary.global <- geary.test(value, listw=nb.idw, zero.policy = TRUE , 
>>> alternative="two.sided")
>>> geary.global
>>> 
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>> 
>> -- 
>> Roger Bivand
>> Department of Economics, NHH Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; fax +47 55 95 95 43
>> e-mail: Roger.Bivand at nhh.no
>> 
>
>
>
> ----------------------------------------------------------------
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-- 
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no