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State space model for geo-locating
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A statistical model to estimate position errors, movement model parameters, and most probable positions from tracking data.
Two add-on packages for the statistical environment R are available.
KFtrack uses only the raw light based geo-locations, which unfortunately often are very uncertain. A simple movement model is assumed. The model parameters are estimated, and the most probable track is reconstructed. The reconstructed track is most often more reasonable and less variable than the raw track.
KFSST uses all the same data that KFtrack does, but it also uses the sea surface temperature. Since water temperatures are commonly stored by the tags, and sea surface temperatures are available from satellite data, it is possible to further improve the reconstruction of the most probable track.UKFSST is an update to KFSST. It uses all the same data as KFSST, but Optimal SST smoothing is determined as part of the model, it uses a better approximation scheme, and partial missing data records are allowed.
Trackit a package to estimate the most probable track directly from the raw light readings in the tag (not the preprocessed geolocations). If SST measurements are also available these can also be used within the same model.
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See: Sibert, John and David Fournier (2001). Possible Methods for Combining Tracking Data with Conventional Tagging Data. In: J.R. Sibert and J. Nielsen (Eds), Electronic Tagging and Tracking in Marine Fisheries (pp. 443-456). Kluwer Academic Publishers, The Netherlands.
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Sibert, J., Musyl, M.K., and Brill, R.W. (2003). Horizontal movements of bigeye tuna (Thunnus obesus) near Hawaii determined by Kalman filter analysis from archival tagging data. Fisheries Oceanography 12:3, 141-151, 2003.
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Nielsen, A., Bigelow, K.A., Musyl, M.K., and , Sibert J.R. (2006). Improving Light-based Geolocation by Including Sea Surface Temperature. Fisheries Oceanography15:4, 314-325.
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Send comments or questions to: sibert@hawaii.edu and andersn@hawaii.edu
Phone: 808-956-7895, FAX: 808-956-4104
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Interactive Tracking Map
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The clever folks from Google have made tools available for creating interactive maps, Google Maps and Google Earth These tools are readily adaptable to the creation of simple interactive geographic displays of tracking data. The kftrack R package provides methods to view tracks using Google Maps and Google Earth. Once a track has be estimated you can invoke write.html(...) to create a web page on your computer than can be viewed with any web browser (such as Firefox). If you wish to see your track on the same map as tracks that researchers from other parts of the world have produced, you can invoke upload.track(...) to upload your track to the very map shown here. Alternatively, you can invoke write.kml(...) to create file that can be viewed using Google Earth.
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BASIC Source Code from Roger Hill and Melinda Braun
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From: Hill, Roger D., and Melinda J. Braun (2001). Geolocation by Light Level - The Next Step: Latitude. In: J.R. Sibert and J. Nielsen (Eds.), Electronic Tagging and Tracking in Marine Fisheries (pp. 315-330). Kluwer Academic Publishers, The Netherlands.
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The following files are for use in calculation of longitude (Appendix A), and of night length (Appendix B):
- Appendix A, BASIC subroutine to determine Equations of Time (text file, 1.16 KB)
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Appendix B, Set of BASIC subroutines to calculate night length (text file, 12 KB)
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Send comments or questions to: tags@wildlifecomputers.com
Phone 425-881-3048, FAX 425-881-3405
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Morpho - Client Metadata Editor
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Morpho is a data management application targeted at ecologists. It is tightly integrated with the Knowledge Network for Biocomplexity, making it easy for ecologists to manage their own data and collaborate with other researchers through the KNB. It includes an advanced data query tool, metadata creation tool, and data management facilities, and, because it is based on Java, works equally well on Windows, Macintosh, and UNIX operating systems. View Morpho User Guide. Morpho requires Java Software be installed.
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MetacatClient - Access Control and Metadata/Data Uploader
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The MetacatClient software is for finer Access Control of the Metadata/Data. Morpho sets one access to the Metadata and Data in a package which means the Metadata and Data have the same access. The MetacatClient allows you to set different access to the Metadata and Data. ie make the Metadata public, but allow only restricted accesss selected users. Although it's primary job is access, it can do Data file uploads and updates. Also, if you prefer to use a command line instead of the gui, it is included with the zip file below. MetacatClient requires Java Software be installed.
Download MetacatClient Zip File [Date Updated: 2006-05-15 11:58:36 -1000 (Mon, 15 May 2006)]
