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Efficient 3D Movement-Based Kernel Density Estimator and Application to Wildlife Ecology

Authors:

Jeff A. Tracey,

James K. Sheppard,

Glenn K. Lockwood,

Amit Chourasia,

Mahidhar Tatineni,

Robert N. Fisher,

Robert S. SinkovitsAuthors Info & Claims

XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment

Article No.: 14, Pages 1 - 8

https://doi.org/10.1145/2616498.2616522

Published: 13 July 2014 Publication History

Abstract

We describe an efficient implementation of a 3D movement-based kernel density estimator for determining animal space use from discrete GPS measurements. This new method provides more accurate results, particularly for species that make large excursions in the vertical dimension. The downside of this approach is that it is much more computationally expensive than simpler, lower-dimensional models. Through a combination of code restructuring, parallelization and performance optimization, we were able to reduce the time to solution by up to a factor of 1000x, thereby greatly improving the applicability of the method.

References

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Hebblewhite, M. and Haydon, D. T. Distinguishing technology from biology: a critical review of the use of GPS telemetry data in ecology. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 365, 1550 (Jul 27 2010), 2303--2312.

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Tomkiewicz, S. M., Fuller, M. R., Kie, J. G. and Bates, K. K. Global positioning system and associated technologies in animal behaviour and ecological research. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 365, 1550 (Jul 27 2010), 2163--2176.

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Sheppard, J. K., Walenski, M., Wallace, M. P., Velazco, J. J. V., Porras, C. and Swaisgood, R. R. Hierarchical dominance structure in reintroduced California condors: correlates, consequences, and dynamics. Behavioral Ecology and Sociobiology 67 (2013), 1227--1238.

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Powell, R. A. and Mitchell, M. S. What is a home range? Journal of Mammalogy 93 (2012), 948--958.

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Spencer, W. D. Home ranges and the value of spatial information. Journal of Mammalogy, 93 (2012), 929--947.

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Silverman, B. W. Density estimation for statistics and data analysis. Chapman and Hall, London; New York, 1986.

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Van Winkle, W. Comparison of several probabilistic home range models. Journal of Wildlife Management 39 (1975), 118--123.

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Worton, B. J. Kernel methods for estimating the utilization distribution in home-range studies. Ecology, 70 (1989), 164--168.

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Fieberg, J. and Börger, L. L. Could you please phrase "home range" as a question? Journal of Mammalogy 93 (2012), 890--902.

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Horne, J. S., Garton, E. O., Krone, S. M. and Lewis, J. S. Analyzing animal movements using Brownian bridges. Ecology, 88, 9 (Sep 2007), 2354--2363.

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Benhamou, S. Dynamic approach to space and habitat use based on biased random bridges. PloS ONE, 6, 1 (2011), e14592.

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Belant, J. L., Millspaugh, J. J., Martin, J. A. and Gitzen, R. A. Multi-dimensional space use: the final frontier. Frontiers in Ecology and the Environment, 10, 1 (2012), 11--12.

[14]

Tracey, J. A., Sheppard, J. K., Zhu, J., Wei, F., Swaisgood, R. R. and Fisher, R. N. Movement-based Estimation and Visualization of Space Use in 3D for Wildlife Ecology and Conservation., PLoS ONE (in revision).

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Jin, H.-W., Sur, S., Chai, L. and Panda, D. K. Limic: Support for high-performance mpi intra-node communication on linux cluster. In IEEE International Conference on Parallel Processing ICPP 2005, (2005).

Digital Library

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Chourasia, A., Wong-Barnum, M. and Norman, M. L. SeedMe preview: your results from disk to device. In Proceedings of XSEDE13 Conference (Atlanta, GA 2013).

Digital Library

Cited By

Dodge SNoi E(2021)Mapping trajectories and flows: facilitating a human-centered approach to movement data analyticsCartography and Geographic Information Science10.1080/15230406.2021.1913763(1-23)Online publication date: 21-May-2021
https://doi.org/10.1080/15230406.2021.1913763
Demšar ULong J(2019)Potential path volume (PPV): a geometric estimator for space use in 3DMovement Ecology10.1186/s40462-019-0158-47:1Online publication date: 29-Apr-2019
https://doi.org/10.1186/s40462-019-0158-4

Index Terms

Efficient 3D Movement-Based Kernel Density Estimator and Application to Wildlife Ecology

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Information

Published In

cover image ACM Other conferences

XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment

July 2014

445 pages

ISBN:9781450328937

DOI:10.1145/2616498

General Chair:
Scott Lathrop
National Center for Supercomputing Applications
,
Program Chair:
Jay Alameda
National Center for Supercomputing Applications

Copyright © 2014 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

In-Cooperation

NSF: National Science Foundation
Drexel University
Indiana University: Indiana University

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 13 July 2014

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XSEDE '14

XSEDE '14: Annual Conference of the Extreme Science and Engineering Discovery Environment

July 13 - 18, 2014

GA, Atlanta, USA

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XSEDE '14 Paper Acceptance Rate 80 of 120 submissions, 67%;

Overall Acceptance Rate 129 of 190 submissions, 68%

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Cited By

Dodge SNoi E(2021)Mapping trajectories and flows: facilitating a human-centered approach to movement data analyticsCartography and Geographic Information Science10.1080/15230406.2021.1913763(1-23)Online publication date: 21-May-2021
https://doi.org/10.1080/15230406.2021.1913763
Demšar ULong J(2019)Potential path volume (PPV): a geometric estimator for space use in 3DMovement Ecology10.1186/s40462-019-0158-47:1Online publication date: 29-Apr-2019
https://doi.org/10.1186/s40462-019-0158-4

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