[AniMov] Clipping area from home range estimates

Anne Ghisla a.ghisla at gmail.com
Mon Jul 13 10:13:54 CEST 2009

Il giorno lun, 13/07/2009 alle 09.49 +0200, Damiano G. Preatoni ha
> 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.

Hi Tim, list,

another method that deserves consideration is Local Convex Hull (LoCoH),
available in package adehabitat. It fits the point dataset better than
kernel, easily excluding non-habitat areas. Have a look at the site [0],
where you can also perform a trial analysis via web.

Anne Ghisla

[0] http://locoh.cnr.berkeley.edu/

Getz, W. and C. Wilmers. 2004. A local nearest-neighbor convex-hull
construction of home ranges and utilization distributions. Ecography 27:
Getz WM, Fortmann-Roe S, Cross PC, Lyons AJ, Ryan SJ, et al (2007)
LoCoH: Nonparameteric Kernel Methods for Constructing Home Ranges
and Utilization Distributions. PLoS ONE 2(2): e207.

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