[AniMov] [SoC09-Idea] Movement Ecology add-ons for adehabitat package
Damiano G. Preatoni
prea at uninsubria.it
Tue Feb 24 15:34:55 CET 2009
here's a proposal for a SoC project on wildlife movement patterns analysis.
A MSc student is available to anwser the call, of course. The idea has already
been briefly discussed with the mantainer of the adehabitat package and the
AniMov project community.
Develop some add-on functions to use the adehabitat package to perform basic
movement ecology analysis, in particular analysis of fractal dimension D.
Developed functions could possibly be included in a future release of the
adehabitat package itself.
Fractal dimension analysis is an useful tool to better understand not just
the 'path tortuosity', in an animal's trajectory, but also the scale level at
which 'search patterns' occur, i.e. an indirect index of the scale at which
habtat resources are 'perceived'.
It has already been shown using simulations (Nams 2005; Oecologia 143:
179-188) that the fractal dimension D of a trajectory changes within scales,
and that the fractal dimension could be a valuable tool in multiscale
analysis of wildlife movement patterns.
The adehabitat package, increasingly used as a free-open source alternative in
radiiotracking and animal habitat selection studies, already has base
functions to deal with trajectories in time and space, both as regular
samples (e.g. data from GPS radio tags) and as irregular ones (as
in 'classic' VHF radiotraking). The implementation of the algorithms devised
by Nams could widen the range of analytical instruments that already make
adehabitat an almost complete tool.
Moreover, the author of the sole existing software to do fractal analysis (V.
O. Nams ) has expressed no objection towards such a porting (as reported
by Paolo Cavallini in the AniMov mailing list ), suggesting that a
complete rewrite could be a better solution.
In detail, the project objectives will be to port (or rewrite) into R
the 'standard' methods offered by the FRACTAL program:
- fractal dimension estimation (D) using the basic divider method
- estimation of D the resampling divider method (Nams 2006: Acta Biotheoretica
- estimation of D using the VFractal estimator (Nams, 1996: Landscape Ecology
- production of other relevant movement ecology statistics useful in spetial
scale perception by animals (Nams 2006: Animal Behaviour. 72: 1197-1203).
- optionally, in conjunction with the random movement simulators already
present in adehabitat (in particular simm.levy and simm.crw), test for
deviations from a CRW model (Nams and Bourgeois 2004: Can J. Zool,
82:1738-1747) and detect if oriented movements occur (Nams 2006: Animal
Behaviour. 72: 1197-1203)
The candidate should be both familiar with R programming and wildlife
radiotracking data analysis. A minimal familiarity with the adehabitat code
could be desirable.
Damiano G. Preatoni, PhD.
Unità di Analisi e Gestione delle Risorse Ambientali
Università degli Studi dell'Insubria
(see signature for details)
And, finally, the programming exercise :
the candidate should demonstrate to be able to transform raw irregular VHF
radiotracking data into an adehabitat ltraj object, which could be the base
data structure to work with in the proposed package.
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