This function calculates a useful measure of similarity between distributions known as the Bhattacharyya coefficient in statistics and simply the fidelity or overlap in quantum and statistical mechanics. It is roughly speaking the ratio of the intersection area to the average individual area, but it is a direct comparison between the density functions and does not require an arbitrary quantile to be specified. When applied to
ctmm objects, this function returns the overlap of the two Gaussian distributions. When applied to aligned
UD objects with corresponding movement models, this function returns the overlap of their (autocorrelated) kernel density estimates.
The confidence level desired for the output.
Approximate debiasing of the overlap.
Additional arguments relevant for
A table of confidence intervals on the overlap estimate. A value of
1 implies that the two distributions are identical, while a value of
0 implies that the two distributions share no area in common. Corresponding
ctmm objects are necessary to provide confidence intervals and debiasing for the point esitmates.
ctmm v0.5.2, direct support for
telemetry objects was dropped and the
CTMM argument was depreciated for
UD objects, simplifying usage.
Uncertainties in the model fits are propagated into the overlap estimate under the approximation that the Bhattacharyya distance is a chi-square random variable. Debiasing makes further approximations noted in Winner & Noonan et al (2018).
C. H. Fleming and K. Winner
K. Winner, M. J. Noonan, C. H. Fleming, K. Olson, T. Mueller, D. Sheldon, J. M. Calabrese. Statistical inference for home range overlap. Methods in Ecology and Evolution, DOI:10.1111/2041-210X.13027 (2018).
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# Load package and data library(ctmm) data(buffalo) # fit models for first two buffalo GUESS <- lapply(buffalo[1:2], function(b) ctmm.guess(b,interactive=FALSE) ) FITS <- lapply(1:2, function(i) ctmm.fit(buffalo[[i]],GUESS[[i]]) ) names(FITS) <- names(buffalo[1:2]) # Gaussian overlap between these two buffalo overlap(FITS) # AKDE overlap between these two buffalo # create aligned UDs UDS <- akde(buffalo[1:2],FITS) # evaluate overlap overlap(UDS)
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