[AniMov] Clipping area from home range estimates

Damiano G. Preatoni prea at uninsubria.it
Mon Jul 13 09:49:17 CEST 2009

In un messaggio del Sunday 12 July 2009, Tim Clark ha scritto:
> Dear List,
> I am trying to use Adehabitat to analyze the home range and movement
> patterns of fish (manta rays, sharks, and various species of reef fish) in
> Hawaii, but have not found a way to clip land area out of the animals home
> range.  Most of the fish I study stay fairly close to shore, moving along a
> sinuous coastline.  I have used adehabitat to estimate their home range (I
> am mostly interested in kernel HR's), but need to either limit the
> calculations to only include water areas during the calculation or clip out
> the land area after the kernel has been calculated.  Is there a way to use
> a shapefile or other projected map file to either limit the kernel or to
> clip out the area post-processing?  I am fairly new to R and adehabitat,
> and am working in Windows.

First, Paolo's suggestion is perhaps the straightforward way: usually, home 
range polygons are clipped in a post-processing phase.

An interesting way I'm testing is to exploit the "grid=" parameter in kernelUD 
(and similar commands).
In fact, since we often have to deal with batch home range calculation on 
several animals scattered on wide study areas, the classical 40x40 squares 
grid is too coarse, resulting in poorly defined polygons.
We overcome this limitation first building a grid (that is a raster) with a 
cell size adequate to the species under study (say, 50x50 m for snowshoe hare 
or bats, 100 to 250 m for ungulates) and supplying that grid (loaded into R 
via import.asc) to the kernelUD command.

On these premises, my suggestion is to prepare a grid already clipped, in your 
case for land against sea. We're trying such a 'trick' to exclude some small 
Alpine lakes in home range calculations on our snowshoe hare dataset.

Hope This Helps

Fallo solamente col migliore.
		-- Dalle Leggi di Murphy sul Sesso
Damiano G. Preatoni, PhD

Unità di Analisi e Gestione delle Risorse Ambientali
Dipartimento Ambiente-Salute-Sicurezza
Università degli Studi dell'Insubria
Via J.H. Dunant, 3 - 21100 Varese (ITALY)

tel +39 0332421538 fax +39 0332421446
ICQ: 78690321 jabber: prea at jabber.org skype: prea.net
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