converting a estUD object to a SpatialGridsPolygon or SpatialPixelsPolygon

Question

I have used the package adehabitatHR in R to estimate the utilization distribution (UD) of a bird using a custom grid

#make the custom grid
x <- seq(-1723705, 2511295, by = 5000) 
y <- seq(7085019, 9240019, by = 5000)
xy <- expand.grid(x=x,y=y)
coordinates(xy) <- ~x+y
gridded(xy) <- TRUE
class(xy)

kde.blsc <- kernelUD(blsc.ptt, h = "href", grid = xy)

#kde.blsc is an `estUD` object
summary(kde.blsc)

I would now like to extract the UD values from kde.blsc to either a SpatialPixelsDataFrame or a SpatialPolygonsDataFrame, so that I can link it to habitat variables saved in a separate SpatialPolygonsDataFrame.

However, when I try to use the function estUDm2spixdf, I get the following error:

blsc.pix <- estUDm2spixdf(kde.blsc)

Error in estUDm2spixdf(kde.blsc) : x should be of class "estUDm"

How can I turn kde.blsc into a estUDm object? Or are there any alternative methods?

Answer 1

Admittedly, the object structures from the adehabitat packages can be very difficult to deal with and are quite obtuse. I believe that in your case, the resulting object is functionally a list object with the class estUD. You should be able to reference an specific KDE (UD) using a double bracket and coerce using as. Try this and let me know if it works.

Load data and estimate UD for the four animals

library(sp)
library(adehabitatHR)

data(puechabonsp)
  loc <- puechabonsp$relocs

( ud <- kernelUD(loc[,1]))
  names(ud)

Extract a specific KDE from the list object and coerce to "SpatialPixelsDataFrame"

ud1 <- as(ud[[1]], "SpatialPixelsDataFrame")
  class(ud1) 
  head(ud1@data) 
  plot(ud1)

If you are wanting to extract pixel values, to get a zonal summary of some sort, you can go straight to a raster class object and then use raster::extract.

library(raster)
  ud1 <- raster(as(ud[[1]], "SpatialPixelsDataFrame"))
    class(ud1) 
    plot(ud1) 
extract(ud1, loc[,1]) # extract point values for x,y used in UD est