[GIS] R – Crop a pixel image produced by spatstat with a boundary shape

cliprspatstat

i am using the very good spatial statistic package spatstat to produce probability maps of spatial point patterns.
Here is a simple working result from the examples to try out.

  require(spatstat)
  data(lansing)
  z <- relrisk(lansing)
  plot(z, main="Lansing Woods")

My question is rather simple (or maybe not). I produced a similar map as shown above and i want to crop it in R with a boundary shapefile. The spatstat package uses its own system (of windows and pixel images) so i am rather clueless. I know that i can format my shapefile to a so called mask with this command as.mask(as.owin(shapefile)), but i didn't get beyond this point.
Anyone knows how i can crop the produced image with this mask?

EDIT:
Ahh, sry. I already found a solution around it, which works for me. I simply have to make a subset out of the spatial points before converting it to a ppp object.

library(rgdal)
st <- readOGR("GIS-Data","boundary_shape") 
wp <- spp[-which(is.na(over(spp,st)[,1])),] # spp is my spatial point shape
rm(st)
#Then use this command from the maptools package
library(maptools)
plp <- as.ppp.SpatialPointsDataFrame(wp)

Nevertheless it would still be nice to know if it is possible to crop a spatstat pixel image.

Best Answer

The best approach is to coerce your spatstat "image" object to an sp object and use the over function or clip in the raster package. Here is a function to perform the coercion to an sp SpatialGridDataFrame.

as.SpatialGridDataFrame.im <- function(from){
    offset=c(from$xrange[1] + 0.5 * from$xstep, from$yrange[1] + 0.5 * from$ystep)
      cellsize = c(diff(from$xrange)/from$dim[2], diff(from$yrange)/from$dim[1])
dim = c(from$dim[2], from$dim[1])
  gt = GridTopology(offset, cellsize, dim)
    m = t(from$v[nrow(from$v):1, ])
  data = data.frame(v = as.vector(m))
SpatialGridDataFrame(gt, data)
}
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