In un messaggio del Wednesday 28 July 2010, Corrie Curtice ha scritto: > On Wed, Jul 28, 2010 at 2:35 AM, Anne Ghisla <[email protected]> wrote: > > On Tue, 2010-07-27 at 15:27 -0400, Corrie Curtice wrote: > >> Hello, > >> > >> I am trying to export the home range for a single individual animal. > >> I'm getting the error "Error in re[[i]] : subscript out of bounds" -- > >> I looked on the archive and found my own posting of this question for > >> the 100% isopleth. :) So now I'm wondering, why does the error occur > >> at lower isopleth levels? Ideally I would like the 95% KHRE to show > >> the "home range" of each animal, and this works with all other > >> individuals. The answer to my last posting noted that the isopleth > >> went beyond the grid limits. I'm not passing in an underlying grid. > >> Here's my call: > >> > >> ud <- kernelUD(xy, grid=100, h="href") > >> kvtmp <- getverticeshr(ud, lev = 95) > >> > >> Levels up to 85 work fine. Is there anything I can do to fix this, if > >> not what is the proper way to report the result for this animal? If > >> you need more code or output I can send. > > > > Hi Corrie, > > > > it sounds like the issue reported here: > > > > https://trac.faunalia.it/animove/ticket/13 > > > > does your dataset show anisotropy? The one attached to the ticket is a > > narrow cloud of points along a horizontal line. The default grid created > > by kernelUD is likely not able to encompass the whole UD. If the case, I > > would try creating a wider grid and providing it to kernelUD. > > > > hope this helps! > > Yes, that's exactly it. I tried increasing the value passed into the > grid parameter -- is this right? Is there some way to determine what > the correct value would be?
There is no "correct" value for the grid parameter.
It it a known "feature" of adehabitat.
That is, passing "grid=<some integer value>" means that kernel calculations
(see e.g. Worton classical text) start with superimposing your point locations
a mesh with <integer value> x <integer value> _cells_. Worton's default is
40x40.
Problem is that is more meaningful having the possibility to supply the _cell
size_ insteda of the _number of cells_.
This means that if your points cloud covers a _wide_ extent, say, half a
state, you will have in your case a 100x100 cells mesh, and a single cell side
will be some tenths of kilometers!
To overcome this problem, one should use "grid=<a kasc object>" (look into
kernelUD source...).
I normally do like this:
- using my favorite GIS package, I create a raster with the cell size I want,
making it so that covers my study area. This way I'll have for instance a
raster with 100 m cells, with a size of such and such rows and columns (I say
'such and such' since we're not interested in how many squares we have, but in
how long is a square side!).
- I export that raster in ASCII GRID format.
- back into R I use read.asc function and create a kasc object that then I
will use as my "reference grid" in home range calculations, like this:
my.reference.grid <- read.asc('refgrid.asc')
ud <- kernelUD(xy, grid=my.reference.grid, h="href")
Hope this helps!
--
Never drink from your finger bowl -- it contains only water.
-----------------------------------------------------------
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
http://biocenosi.dipbsf.uninsubria.it/
ICQ: 78690321 jabber: [email protected] skype: prea.net
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