Convert from spatialpixeldataframe to estUD - r

Question

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"

Answer 1

Where we have
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]]