adehabitat​HR: calculatio​n of UDOI using adaptive and fixed kernels

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adehabitat​HR: calculatio​n of UDOI using adaptive and fixed kernels

James Garabedian
Dear list,



I am trying to quantify the utilization distribution overlap index (UDOI;
e.g., Fieberg and Kochanny 2005) for several birds using the package
adehabitatHR (v. 0.4.2). I have already generated utilization distributions
(UD) for the birds using adaptive and fixed kernel methods in Animal Space
Use (Horne and Garton 2006a, Horne and Garton 2006b, Horne and Garton
2007). Specifically, the information theoretic approach available in Animal
Space Use was used to determine the most appropriate method to estimate
home ranges for each of our birds, which resulted in a mix of adaptive and
fixed kernels. Preferably, I would like to pass the UDs generated in Animal
Space Use to the function kerneloverlap (or perhaps kerneloverlaphr) in
adehabitatHR, but I can’t find the methods/documentation to do so.



Alternatively, I could generate UDs using the kernelUD function in
adehabitatHR. However, as far as I can tell, adaptive and fixed kernel
methods are not available in the kernelUD function.



A sample of the UD data (output as a .txt) from Animal Space Use for two
birds (I added “Name”):

         X                 Y              Name          Probability

3687857.115   452370.15       A         0.000000002

3687857.115   452371.85       A         0.000000002

3687857.115   452373.55       A         0.000000003

3687857.115   452375.25       A         0.000000003

3687857.115   452376.95       A         0.000000003

3687857.115   452378.65       A         0.000000003

…

3687875.5       452350.31       B          0.000000031

3687875.5       452352.05       B          0.000000039

3687875.5       452353.79       B          0.000000048

3687875.5       452355.53       B          0.00000006

3687875.5       452357.27       B          0.000000073

3687875.5       452359.01       B          0.000000088



My questions:

1)      Is there a way to pass the UDs generated in Animal Space Use to
kerneloverlap/kerneloverlaphr in adehabitatHR? If so, how might I go about
that?
2)      If currently there is no solution to my first question, is there a
way use adaptive and fixed kernel methods to generate UDs using kernelUD?

I am using R version 2.14.2.


Thanks in advance,


James

Fieberg, J., and C.O. Kochanny. 2005. Quantifying home-range overlap: the
importance of the utilization distribution. Journal of Wildlife Management
69:1346–1359.
Horne, J.S., and E.O. Garton. 2006a. Selecting the best home range model:
an Information Theoretic approach. Ecology 87: 1146–1152.
Horne, J.S., and E.O. Garton. 2006b. Likelihood cross-validation versus
least squares cross-validation for choosing the smoothing parameter in
kernel home-range analysis. Journal of Wildlife Management 70: 641–648.
Horne, J.S., and E.O. Garton. 2007. Animal space use 1.3. Available at: <
http://www.cnr.uidaho.edu/population_ecology/animal_-space_use.htm.>
Accessed 16 Nov 2011.


--
James Garabedian
Research Assistant
 North Carolina State University
Dept. of Forestry and Environmental Resources
[hidden email]
Office: (803) 652-3632
Fax: (803) 652-8315

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Re: adehabitat​HR: calculatio​n of UDOI using adaptive and fixed kernels

JLong
James:

1)      Is there a way to pass the UDs generated in Animal Space Use to
kerneloverlap/kerneloverlaphr in adehabitatHR? If so, how might I go about
that?

You could save your UD's from Horne & Garton's toolkit as rasters then check out this thread b/w Tony Fischbach and Clement Calenge
http://r-sig-geo.2731867.n2.nabble.com/Walruses-and-adehabitatHR-class-estUDm-exclusion-of-non-habitat-pixels-and-summary-over-all-animals-td6497315.html#none


2)      If currently there is no solution to my first question, is there a
way use adaptive and fixed kernel methods to generate UDs using kernelUD?


The kernelUD function is a fixed kernel method, I don't believe there is an adaptive kernel option however.


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Jed Long
Lecturer in GeoInformatics
Department of Geography & Sustainable Development
University of St Andrews, UK