[R-sig-Geo] Estimation of utilization distribution and home range within a polygon

[Manuel Spínola]

Thank you very much Michael and Tom.

Best,

Manuel

2016-08-15 17:18 GMT-06:00 Tom Philippi <tephilippi at gmail.com>:

> Manuel--
> I don't think that there is one single "right" method for estimating
> homeranges or spatial utilization contours with spatial boundaries.
>
> Before deciding on the computations, I would encourage you to carefully
> think about and define how movement & spatial utilization react to the
> polygon boundaries.  Are the boundaries the equivalent of a sheer wall,
> where individuals use space normally right up to the boundary, or is there
> a gradient of repulsion extending some (short) distance from the boundary
> (e.g., too shallow water) so use drops off a bit before the boundary, or is
> the boundary attractive or reflecting, where potential movements across the
> boundary become repeated head-banging against the boundary (e.g., desert
> tortoises and other herps hitting drift fences)?
>
> At the micro-scale, your pdf from each fish position is something like a
> 2-d Epanechnikov or normal bump of volume 1/N.  If that bump spans (or even
> gets near to) your boundary, you probably want the volume to remain 1/N.
> The options may be to clip at the boundary & renormalize by a scalar to
> retain 1/N, or shift to an anisotropic kernel elongated along the
> boundary.  Just doing the full  kernelling and then clipping the homerange
> reduces the weight given to that observation near the boundary relative to
> the other observations, biasing your estimated utilization away from the
> edges.  For places like the Everglades where water depth, nutrients, and
> vegetation are very different near the edges of wetland compartments, that
> bias would be seriously misleading.
>
>  Perhaps none of this matters for the spatial scales of your fish,
> boundary effects in your wetlands, and the frequency of position locations
> of individual fish (with 1000 observations per fish, fractionally
> downweighting a couple of observations has little effect).
>
> My suggestion can be thought of as an expansion of Mike's: "You can just
> clip after the fact, but as you surely know that defeats the
> purpose if the boundary has meaning to the intensity of behaviour" above
> to cases beyond just clipping.  Mike is both more succinct and faster at
> responding than I am.
>
> Tom 2
>
> On Mon, Aug 15, 2016 at 8:38 AM, Michael Sumner <mdsumner at gmail.com>
> wrote:
>
>> It sounds like maybe your input constraint is not in a form that kernelUD
>> likes, perhaps there is room to read about the error message and explore
>> the details?
>>
>> You otherwise will need more specialist methods to model within a complex
>> boundary.
>>
>> The soapfilm tools in mgcv is one example:
>> http://www.fromthebottomoftheheap.net/2016/03/27/soap-film-smoothers/
>>
>> Some of the trajectory/ tracking packages probably have stuff, review the
>> packages in the list here:
>>
>> https://cloud.r-project.org/web/views/SpatioTemporal.html
>>
>> There are few other related packages on CRAN from recent times not on that
>> list, and many there have had some significant development so worth
>> exploring.
>>
>> You can just clip after the fact, but as you surely know that defeats the
>> purpose if the boundary has meaning to the intensity of behaviour.
>>
>> (tripEstimation does facilitate this generally,  but I'd say that's much
>> too specialist and buried too deep to be helpful).
>>
>> Cheers, Mike.
>>
>> On Tue, 16 Aug 2016 at 01:08 Manuel Spínola <mspinola10 at gmail.com> wrote:
>>
>> > Dear list members,
>> >
>> > Is there a way to estimate utilization distribution and home range area
>> > within a polygon.  I am working with spatial location on a fish in a
>> > wetland but the utilization distribution and the home range cannot go
>> > outside the water boundary.
>> >
>> > I tried using a spatial polygon as spatial line and specify this in the
>> > boundary argument of the kernelUD function of the adehabitatHR package
>> but
>> > I got an error:
>> >
>> > > ud = kernelUD(dfs_in[,2], h="href", grid = 100, boundary = riol)
>> >
>> > Error in .boundaryk(SpatialPoints(x, proj4string =
>> > CRS(as.character(pfs1))),  :
>> >   non convenient boundary: turning angles > pi/2
>> >
>> > "riol" is the spatial polygon coerced to spatial line
>> >
>> > Thank you very much in advance
>> >
>> > Manuel
>> >
>> > --
>> > *Manuel Spínola, Ph.D.*
>> > Instituto Internacional en Conservación y Manejo de Vida Silvestre
>> > Universidad Nacional
>> > Apartado 1350-3000
>> > Heredia
>> > COSTA RICA
>> > mspinola at una.cr <mspinola at una.ac.cr>
>> > mspinola10 at gmail.com
>> > Teléfono: (506) 8706 - 4662
>> > Personal website: Lobito de río <
>> > https://sites.google.com/site/lobitoderio/>
>> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
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>>
>> --
>> Dr. Michael Sumner
>> Software and Database Engineer
>> Australian Antarctic Division
>> 203 Channel Highway
>> Kingston Tasmania 7050 Australia
>>
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>>
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>
>


-- 
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
mspinola at una.cr <mspinola at una.ac.cr>
mspinola10 at gmail.com
Teléfono: (506) 8706 - 4662
Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>

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