[R-sig-Geo] placing spdf back into adehabiatHR estUDm

[Clement Calenge]

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 at h <- list(h=0, meth="specified") # fake value
     so at 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