I am probably misunderstanding something (as usual) but I cannot fathom
what you *expect* the values of the funxy object or the image to *be*,
outside of the window.
See inline below.
On 16/12/17 08:37, Christopher W. Ryan wrote:
Using R 3.3.3 and spatstat 1.50-0 on Windows 7. MWE below.
Thank you for providing a clear and simple example.
I have a SpatialPolygonsDataFrame of census tract poverty levels in 3
contiguous counties in the US, called sremsPoverty. I want to use this
as a predictor in a ppm model. The window for the point pattern is the
three counties--so an irregular polygon--called sremsWindow.
I understand ppm predictors need to be an image, a tesselation, a funxy,
a window, or a single number. So I proceed as follows:
### Poverty
p <- slot(sremsPoverty, "polygons")
v <- lapply(p, function(z) { SpatialPolygons(list(z)) })
sat <- tess(tiles = lapply(v, as.owin) )
pov.f <- as.function.tess(sat, values = sremsPoverty@data$propPoverty)
Thus pov.f is a spatial function (funxy) that I can use in a call to ppm():
m1 <- ppm(unique.cases.ppp ~ pov.f)
pov.f looks as expected when I plot it. But examing the structure of
as.im(pov.f) it appears it is a 128 x 128 pixel array, with the value of
the function at all pixels outside of the irregular polygonal window,
but inside the bounding rectangle, set to NA.
What else could/should they be set to?
I think this is the cause
of the NA values I am seeing among the residuals from m1,
I don't think this is the case. Perhaps more detail is needed; perhaps
Adrian or Ege will be able to provide more insight.
and those NA
residuals are causing me some trouble with model diagnostics such as
rhohat().
Again I, at least, would need more detail before being able to provide
any constructive comment.
How do I constrain the funxy (or the image I can derive from it) to the
irregular polygonal window, so as to eliminate the NA values outside the
window but inside the bounding rectangle? Or can I constrain the
modeling activity of ppm() to the window?
The "modelling activity of ppm()" is *ALWAYS* constrained to the window
of the pattern to which ppm() is applied. This is fundamental to the
the way that ppm() works, and to what a window *means*.
Thanks.
--Chris Ryan
Broome County Health Department
Binghamton University
SUNY Upstate Medical University
Binghamt, NY, US
MWE:
x <- c(0, 2.6, 3, 1, 0)
y <- c(1,2,3,2,1)
test.window <- owin(poly=list(x=x,y=y))
plot(test.window) ## looks as expected
## make spatial function
test.f <- function(x,y){x+y}
test.funxy <- funxy(test.f, W = test.window) ## I *thought* this would
restrict the funxy to the window, but I don't think it does
plot(test.funxy) ## looks as expected
## but the image from test.funxy is square, with NA values outside the
polygonal window, which is not square
test.im <- as.im(test.funxy)
str(test.im)
Again, what could the values of the image, outside of test.window,
possibly *be*, other than NA?
## my incorrect attempts to restrict the image to the window yields a
numeric vector
str(test.im[test.window])
You need to do
new.im <- test.im[test.window,drop=FALSE]
to get an image rather than a numeric vector. However the "new.im" that
you obtain will be identical to test.im:
> all.equal(new.im,test.im)
[1] TRUE
## or an error message
window(test.im) <- test.window
You need a capital "W" on Window(test.im) (to avoid an error message).
But again this won't change anything.
Finally:
set.seed(42)
X <- runifpoint(20,win=test.window)
xxx <- ppm(X ~ test.im)
plot(residuals(xxx))
# No sign of any missing values.
cheers,
Rolf Turner
--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
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