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

Kerstin Traut Kerstin.Traut at uni-jena.de
Thu Jul 12 17:56:10 CEST 2012 

Zitat von Roger Bivand <Roger.Bivand at nhh.no>:

> 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:
>>>
>>>> Zitat von Roger Bivand <Roger.Bivand at nhh.no>:
>>>>
>>>>> On Thu, 12 Jul 2012, Roger Bivand wrote:
>>>>>
>>>>>> 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.
>>>>>
>>>>> The latter advice may not work if your coordinates are planar  
>>>>> and you really mean to set torus=TRUE in cell2nb(). You'll have  
>>>>> to get the data order right by deconstructing the region.id  
>>>>> attribute of the nb object created by cell2nb() to ensure data  
>>>>> integrity.
>>>>>
>>>>> Roger
>>>>
>>>> I already tested dnearneigh(), but I like to avoid this function  
>>>> because for large datasets cell2nb() calculates neighbors more  
>>>> quickly.
>>>> Thanks to your suggestion I was able to subset the nb list by  
>>>> using nb.subset(). But I could not find a suitable function for  
>>>> subsetting a listw. Using the subset() function results in the  
>>>> following error message: "Not yet able to subset general weights  
>>>> lists". Do you have an explaination?
>>>
>>> Yes, because the changes may not be appropriate, depending on how  
>>> the general weights were defined. In your case, subset the nb  
>>> object and the list of idw weights, and rebuild the listw object  
>>> with the subsetted objects.
>>>
>>> Roger
>>
>> That´s what I already tried, but the error message says "neighbors  
>> and glist do not conform"??
>
> Right, you'll need to rebuild from the subsetted nb object from the  
> nbdists() step (and subsetted coordinates), because the subsetted  
> idw list will have weights for excluded observations.
>
> Roger

Ok, I hope I understood everything right. You mean, firstly, I need to  
subset my nb list and afterwards, I need to calculate the nb-distances  
using nbdists()?

Kerstin


>>
>> Kerstin
>>
>>>>
>>>> Kerstin
>>>>
>>>>
>>>>>>
>>>>>> 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
>>>>>>>>>
>>>>>>>>> ----------------------------------------------------------------
>>>>>>>>> This message was sent through https://webmail.uni-jena.de
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> R-sig-Geo mailing list
>>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ----------------------------------------------------------------
>>>>>>> This message was sent through https://webmail.uni-jena.de
>>>>>>
>>>>>>
>>>>>
>>>>> -- 
>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>> ----------------------------------------------------------------
>>>> This message was sent through https://webmail.uni-jena.de
>>>
>>> -- 
>>> 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
>>>
>>
>>
>>
>> ----------------------------------------------------------------
>> This message was sent through https://webmail.uni-jena.de
>
> -- 
> 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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