[R-sig-Geo] Dealing with lakes and NA in Moran/SpatialPolygonsDataFrame

[Roger Bivand]

On Thu, 3 Sep 2009, Matthieu Stigler wrote:

> Hi
>
> I'm puzzled hot to deal with NAs and lakes on SpatialPolygonsDataFrame
> objects...
>
> My problems (maybe should I post in separated files?):
> -spplot does not seem to handle specially NA values...
> -neighbors graph seem to make links even to lakes/holes
> -moran.test seem to work with NA values... but what about the
> neighbors/weights used as input? Are the results biased?
> -localmoran does not seem to work with NA
>
> I illustrate each of them below.
>
>
> Example is based on Syracuse data from ASDAR (data from web-site
> http://www.asdar-book.org/bundles/lat1_bundle.zip):
> #NA PROBLEM
> setwd("H:/Documents/Stats/Book Bivand/Chap 9")
> library(sp)
> library(rgdal)
> NY8 <- readOGR(".", "NY8_utm18")
> library(spdep)
> Syracuse <- NY8[NY8$AREANAME == "Syracuse city",]
> Syracuse2<-Syracuse
> Syracuse2$POP8[43]<-NA
> spplot(Syracuse2, zcol="POP8")
> #it appears as white, similar to other colors which are nevertheless
> true values and not NA!

NAs are coded "transparent", which look the same when the background is 
white. In the default divergent palette, white is used. If you do:

library(lattice)
trellis.device(bg="grey")
spplot(Syracuse2, zcol="POP8")

(wrong way to change background but OK to show the point) or

trellis.par.set(sp.theme())
spplot(Syracuse2, zcol="POP8")

where white is not in the palette.

>
> LAKE problem:
> #check if lakes:
> sapply(sapply(slot(Syracuse, "polygons"),function(x) slot(x,
> "Polygons")), function(x) slot(x, "hole"))
> #btw, it is pretty complicated, are there some more user-friendly
> wrapers for that? kind of isHole, getHole?

Holes are easy to fall into, so no wrappers.

> slot(slot(slot(Syracuse2, "polygons")[[43]],"Polygons")[[1]], "hole")<-TRUE
> plot(poly2nb(Syracuse), coordinates(Syracuse2))

poly2nb() uses all the geometries present. The prefered choice is to 
subset the geometries to keep only the ones the user requires, so:


not_holes <- !sapply(sapply(slot(Syracuse2, "polygons"),function(x)
   slot(x, "Polygons")), function(x) slot(x, "hole"))
nb <- poly2nb(Syracuse2[not_holes,])
plot(nb, coordinates(Syracuse2)[not_holes,])

I guess this clarifies things. In principle, a single Polygon object in a 
Polygons object will not be a hole anyway (it is an external ring), so 
your example is rather artificial. Subsetting the geometries with "[" is 
to be prefered.

Hope this helps,

Roger

I guess the same applies to your followup - but spautolm() ought not to 
permit computation on missing data - I'll check this.

>
> Here it seems that it did not take into account the hole and still
> computes neighbors... right?
>
> And if yes... does it affect the results using moran tests?
>
> Thanks a lot!
> Matthieu Stigler
>
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-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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