Dear Antony,
You are right, there is indeed a problem with the object estUDm returned
by the function BRB. As you rightly noted, each estUD object has a full
listing of the D values from all animals (which does not impair the use
of other functions, but indeed need to be corrected), and the estUD
objects are not named (which does impair the use of this object in other
functions, e.g. getverticeshr). For the last bug, as you noted, an easy
workaround consists in manually defining these names (I will correct
this bug ASAP). Many thanks for reporting.
Now, concerning your "clipping problem".
## Note that Brock and Calou, the UD have sharp limits
###ASF### Yes I see this.
This is because the extent of the grid is to small, compared with the
size of the UD (or maybe your smoothing parameters are too large). In
your example, the map contained in puechabonsp is too small and does not
encompass all possible locations where the animals may have moved, given
the diffusion and smoothing parameters that you defined. Another map,
larger, would therefore be required. Note that if your aim is just to
calculate home range contours, you do not need to use this map: you
should define another grid with a larger extent, and then (see the
parameters grid and extent on the help page of BRB). If your aim is to
measure the use intensity in each pixel of the habitat map, then you do
not need home ranges limits.
###ASF### [2011 August 05]: Questions for ClementCalenge:
###ASF### ???? How can we extract home-range contours now that the home
range estimates are of class SpatialPixelsDataFrame?
The class estUDm is simply a list of objects of class estUD. And an
object of class estUD is simply a SpatialPixelsDataFrame with additional
slots h (a list of two specifying how h is computed) and vol. Therefore,
the following should work, using your objects:
fullgrid(udspdf) <- FALSE
re <- lapply(1:ncol(udspdf), function(i) {
so <- new("estUD", udspdf[,i])
so@h <- list(h=0, meth="specified") # fake value
so@vol <- FALSE
return(so)
})
names(re) <- names(udspdf)
class(re) <- "estUDm"
image(re)
## and find the contours
ver <- getverticeshr(re, standardize=TRUE)
plot(ver)
HTH,
Clément Calenge
--
Clément CALENGE
Cellule d'appui à l'analyse de données
Direction des Etudes et de la Recherche
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14
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