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In short: I have a spatialpixeldataframe of a utilization distribution of an animal across a grid (udspdf) which I need to convert to estUD-class.

Background to how I got there: After calculating the KDE of a single animal, I then need to convert the estUD-class object to a spatialpixeldataframe in order to remove non-habitat cells, and rescale the utilisation distribution of the habitat-cells to 1. I then need to convert the spatialpixeldataframe back to an estUD class file so that I can run kerneloverlaphr() on it.

I have the following code, which converts it to an estUDm-class. But I need it in estUD-class, as there is only one animal.

re <- lapply(1:ncol(udspdf), function(i) {
  so <- new("estUD", udspdf[,i])
  so@h <- list(h=0, meth="specified") # specify dummy h values: they are only required to recreate the estUDm
  so@vol <- FALSE
  return(so)
names(re) <- names(udspdf)
class(re) <- "estUDm"
image(re)
If I just change
class(re) <- "estUD"
This seems to work, but then I can see there is an issue because
image(re)
renders the following error: Error in is(x, "GridTopology") :
trying to get slot "grid" from an object (class "estUD") that is not an S4 object
I am sorry I do not know how to provide a reproducible example for such an example as the data is quite complex. I hope that a general code exists.
Any pointers appreciated!
> str(re)
List of 1
 $ ud:Formal class 'estUD' [package "adehabitatHR"] with 9 slots
  .. ..@ h          :List of 2
  .. .. ..$ h   : num 0
  .. .. ..$ meth: chr "specified"
  .. ..@ vol        : logi FALSE
  .. ..@ data       :'data.frame':  4400000 obs. of  1 variable:
  .. .. ..$ ud: num [1:4400000] 0 0 0 0 0 0 0 0 0 0 ...
  .. ..@ coords.nrs : num(0) 
  .. ..@ grid       :Formal class 'GridTopology' [package "sp"] with 3 slots
  .. .. .. ..@ cellcentre.offset: Named num [1:2] -70 -60
  .. .. .. .. ..- attr(*, "names")= chr [1:2] "Var2" "Var1"
  .. .. .. ..@ cellsize         : Named num [1:2] 0.01 0.01
  .. .. .. .. ..- attr(*, "names")= chr [1:2] "Var2" "Var1"
  .. .. .. ..@ cells.dim        : Named int [1:2] 2000 2200
  .. .. .. .. ..- attr(*, "names")= chr [1:2] "Var2" "Var1"
  .. ..@ grid.index : int [1:4400000] 1 2 3 4 5 6 7 8 9 10 ...
  .. ..@ coords     : num [1:4400000, 1:2] -70 -70 -70 -70 -70 ...
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : NULL
  .. .. .. ..$ : chr [1:2] "Var2" "Var1"
  .. ..@ bbox       : num [1:2, 1:2] -70 -60 -50 -38
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr [1:2] "Var2" "Var1"
  .. .. .. ..$ : chr [1:2] "min" "max"
  .. ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
  .. .. .. ..@ projargs: chr "+proj=longlat +datum=WGS84 +no_defs"
 - attr(*, "class")= chr "estUDm"
my code for kerneloverlaphr(), which works with the outputs stright from kernelUD() (estUD-class) is as follows:
NWI15b, BCI15b and BCI15i are my individual animals
    library(adehabitatHR)
    # convert list of KDEs (estUDs) to class estUDm
    tot <- list(NWI15b=NWI15b, BCI15b=BCI15b, BCI15i=BCI15i)
    class(tot) <- "estUDm"
    #calculate overlap using kerneloverlaphr
    kerneloverlaphr(tot, method = c("BA"), percent = 95, conditional = FALSE)
dput(head(as.data.frame.estUD(re), n = 10))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': no method or default for coercing “estUDm” to “SpatialPixelsDataFrame”
> unique(re@data$ud)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unique': trying to get slot "data" from an object (class "estUDm") that is not an S4 object 
structure of object fed to kernelUD
    str(track_sp)
    Formal class 'SpatialPoints' [package "sp"] with 3 slots
      ..@ coords     : num [1:9790, 1:2] -59.2 -59.2 -59.2 -59.2 -59.2 ...
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : chr [1:9790] "1" "2" "3" "4" ...
      .. .. ..$ : chr [1:2] "x" "y"
      ..@ bbox       : num [1:2, 1:2] -65.8 -55.6 -56.1 -52.2
      .. ..- attr(*, "dimnames")=List of 2
      .. .. ..$ : chr [1:2] "x" "y"
      .. .. ..$ : chr [1:2] "min" "max"
      ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
      .. .. ..@ projargs: chr "+proj=longlat +datum=WGS84 +no_defs"
                Yes, but I do not want to run the kernelUD on it. I have provided more background info in my question to explain why. Thanks!
– user303287
                May 18, 2022 at 18:54
                Well, just telling re that it is class estUD doesn't provision slots, while your code conforms to that detailed R-sig-Geo for revision of SPDF to estUD. My read, as to one animal, is that SpatialPoints are desired rather than SPDF, as (i guess) SPDF implies more or many animals...What does str(re) on the re <- lapply show, and put above. Thanks. and indeed estUD likely required by kernaloverlaphr(), but step by step.
– Chris
                May 18, 2022 at 20:09
re <- lapply(1:ncol(udspdf), function(i) {
so <- new("estUD", udspdf[,i])
so@h <- list(h=0, meth="specified") # specify dummy h values: they are only required to recreate the estUDm
so@vol <- FALSE
return(so)
> names(re) <- names(udspdf)
> class(re) <- "estUDm"
> image(re)
We then need to simply add this:
colonyA <- re[[1]]
#and then do the same after running the code for the next colony
colonyB<- re[[1]]
        
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