R help - Oct 2009 - Spatstat: xy binary data into mask type to use in owin(mask=)

Dear users,

I am trying to export polygons from Arcmap into Spatstat to run some
simulations using functions available in Spatstat package.

One particular area to be exported is formed by a number of polygons
defining the external boundaries of the area (as a groups of islands) and a
number of polygons inside the previous ones,  as ?holes? not to be
considered as part of the area.

I have managed to export one of these areas using owin(poly=list()),
including in the list the number of external boundaries and holes, but the
number of polygons that constitute each area is large and I was wondering if
this could be easily done using owin(mask=my_area), using only one single
matrix file "my_area" with TRUE, FALSE values defining the whole area.

Here is where I got stuck. The file I have created in ArcMap contains three
columns: x and y coordinates, and the values at points x[i], y[j] (1 if the
area is TRUE and 0 is the area is FALSE).

How can I covert this xy file into a mask type "my_area" that I can
read
using owin(mask=my_area)?

Many thanks in advance

Javier     

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On 20/10/2009, at 2:06 AM, Javier PB wrote:
> Dear users,
>
> I am trying to export polygons from Arcmap into Spatstat to run some
> simulations using functions available in Spatstat package.
>
> One particular area to be exported is formed by a number of polygons
> defining the external boundaries of the area (as a groups of  
> islands) and a
> number of polygons inside the previous ones,  as ?holes? not to be
> considered as part of the area.
>
> I have managed to export one of these areas using owin(poly=list()),
> including in the list the number of external boundaries and holes,  
> but the
> number of polygons that constitute each area is large and I was  
> wondering if
> this could be easily done using owin(mask=my_area), using only one  
> single
> matrix file "my_area" with TRUE, FALSE values defining the whole
area.
>
> Here is where I got stuck. The file I have created in ArcMap  
> contains three
> columns: x and y coordinates, and the values at points x[i], y[j]  
> (1 if the
> area is TRUE and 0 is the area is FALSE).
>
> How can I covert this xy file into a mask type "my_area" that I
can
> read
> using owin(mask=my_area)?
It's not clear to me that you can --- it depends on the nature of the  
points
specified by x[i] and y[j].  If these are equispaced then I think you  
can
do it.

Suppose that you have a data frame ``X'' with columns ``x'',
``y'', and
``value'', where value is logical.  Suppose also that the unique values
of x are equispaced on [a,b] and the unique values of y are equispaced
on [c,d].  Finally suppose that *all* possible pairs of (x[i],y[j])
coordinates appear in your data frame X, i.e. nrow(X) = m*n where
m = the number of unique values of x and n = the number of unique values
of y.  Then you can create a mask from X as follows:

# Begin
	m <- as.mask(xy=X[,c("x","y")])
	ij <- with(X,nearest.raster.point(x[!value],y[!value],m))
	m$m[do.call(cbind,ij)] <- FALSE
# End

(Note that even if X$value is left as a numeric vector of 1's and 0's,
``!value'' will coerce it to logical appropriately.)

This will give you a window of type mask with bounding box [a,b] x [c,d]
which will ``be TRUE'' at those pixel centers (x[i],y[j]) where the
corresponding value of ``value'' is TRUE, and FALSE otherwise.

E.g.

	x0 <- seq(1,2,length=40)
	y0 <- seq(2,6,length=50)
	X  <- expand.grid(x=x0,y=y0)
	set.seed(42)
	X$value <- sample(c(TRUE,FALSE),2000,TRUE,prob=c(0.8,0.2))

Then do the three lines between # Begin and # End.  Then do

	plot(m)

to make sure it looks as it should.

There may be a sexier way of accomplishing the task.  If there is,
perhaps Adrian will chip in.

HTH.

	cheers,

		Rolf Turner
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