Hi all,
The result is a non-symmetric distance matrix, which eventually can be
aggregated to have, say, average overlaps between sexes, seasons, etc..
In practice, all that is done with a slightly modified version of Clément's
kerneloverlap. the modification consists in commenting put the first rows
that call kernelUD, and making function kerneloverlap work on already
calculated UDs.
This raises another point, i.e. a suggestion to Clément: since often the 40x40
cells approach gives undesirable results, we prefer to prepare as a
preliminary step, a raster (of course using exclusively ESRI software, duh!)
with cells of suitable size, that encompassess an extent slightly wider than
the study area, an then calculate once all the UDs.
Note that controlling the grid can be done with kerneloverlap: this
functions accepts all the arguments of kernelUD. For example, using the
puechabon dataset:
data(puechabon)
## With 200x200 grid
kerneloverlap(puechabon$locs[,c("X","Y")], puechabon$locs$Name,
grid=200, meth="VI", conditional=TRUE)
## With a map available in R
map <- getkasc(puechabon$kasc,1)
kerneloverlap(puechabon$locs[,c("X","Y")], puechabon$locs$Name,
grid=map, meth="VI", conditional=TRUE)
This 'single point of homerange truth' [2] guarantees a consistency between
subsequant calculations, i.e. 'getvoumes + polygon extraction', compana,
kerneloverlapd etc.
This also saves lots of time, since UD calculation, moreover with a 'fine'
grid, takes some time: UD processing can be done on a fast number crunching
machine [3], and the result can be saved (as part of a sahrlocs structure)
and retrieved on a less performant host to do other postprocessing.
Yes, you are right: kernel UDs are often computed as a basis for further
analysis, including kernel overlap, but not only... It would be more
sensible to estimate UD once, and then using them for other analyses. I
planned to upload a new version of adehabitat to CRAN before the end of
the week, and I will include, on the help page of kerneloverlap, a new
function accepting a "khrud" object to perform this computation.
Many thanks for the suggestion,
Regards,
Clément
--
Clément CALENGE
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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