Assessing Performance of Bayesian State-Space Models Fit to Argos Satellite Telemetry Locations Processed with Kalman Filtering
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{"title"=>"Assessing performance of Bayesian state-space models fit to argos satellite telemetry locations processed with kalman filtering", "type"=>"journal", "authors"=>[{"first_name"=>"Mónica A.", "last_name"=>"Silva", "scopus_author_id"=>"17135969500"}, {"first_name"=>"Ian", "last_name"=>"Jonsen", "scopus_author_id"=>"6603341226"}, {"first_name"=>"Deborah J.F.", "last_name"=>"Russell", "scopus_author_id"=>"28167828300"}, {"first_name"=>"Rui", "last_name"=>"Prieto", "scopus_author_id"=>"22986226300"}, {"first_name"=>"Dave", "last_name"=>"Thompson", "scopus_author_id"=>"55613238449"}, {"first_name"=>"Mark F.", "last_name"=>"Baumgartner", "scopus_author_id"=>"23987658600"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84924584925", "sgr"=>"84924584925", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0092277", "pmid"=>"24651252", "isbn"=>"1932-6203", "pui"=>"607990605"}, "id"=>"16e9631d-74da-31f0-b2a3-ebeefb9e4d78", "abstract"=>"Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (Phoca vitulina) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to \"true\" GPS locations. Data on 6 fin whales (Balaenoptera physalus) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were <5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6±5.6 km) was nearly half that of LS estimates (11.6±8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales' behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.", "link"=>"http://www.mendeley.com/research/assessing-performance-bayesian-statespace-models-fit-argos-satellite-telemetry-locations-processed-k", "reader_count"=>120, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Researcher"=>41, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>5, "Student > Master"=>20, "Other"=>9, "Student > Bachelor"=>7, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Researcher"=>41, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>5, "Student > Master"=>20, "Other"=>9, "Student > Bachelor"=>7, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Engineering"=>2, "Environmental Science"=>19, "Mathematics"=>2, "Agricultural and Biological Sciences"=>82, "Chemistry"=>1, "Social Sciences"=>2, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>82}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>19}}, "reader_count_by_country"=>{"New Zealand"=>1, "Canada"=>2, "Argentina"=>1, "United States"=>3, "Denmark"=>1, "Brazil"=>1, "United Kingdom"=>3, "Mexico"=>1, "South Africa"=>1, "Germany"=>1, "Iceland"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1429091"], "description"=>"<p>Differences in locations estimated from switching state-space models fit to Kalman filtered (KF) (red dots) data are plotted as offsets from locations calculated from the same models fit to Least Squares (LS) data. Standard ellipses were fitted to 95% of KF data points. A. Fin whales #80702 (red), #80704 (blue) and #80707 (green). B. Fin whales #80713 (black), #89969 (orange). C. Fin whale #80716 (pink).</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "locations", "kf", "ls", "fin"], "article_id"=>969101, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.g005", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differences_in_locations_estimated_from_KF_and_LS_models_for_all_fin_whales_/969101", "title"=>"Differences in locations estimated from KF and LS models for all fin whales.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429090"], "description"=>"<p>Predicted error in harbour seal locations according to the best fitting linear mixed-effects model for A. State-space models fit to Kalman filtered (KF) data. B. State-space models fit to Least Squares (LS) data.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "locations", "ls", "kf"], "article_id"=>969100, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_error_in_locations_estimated_from_LS_and_KF_models_/969100", "title"=>"Predicted error in locations estimated from LS and KF models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429086"], "description"=>"<p>Errors in harbour seal locations estimated from state-space models fit to Least Squares (LS) (black) and Kalman filtered (KF) (red) data are plotted as offsets from “true” GPS positions. Standard ellipses were fitted to 95% of LS (black line) and KF (red line) error points.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "locations", "ls", "kf"], "article_id"=>969096, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Errors_in_locations_estimated_from_LS_and_KF_models_/969096", "title"=>"Errors in locations estimated from LS and KF models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429099"], "description"=>"<p>*Variation in mean errors was calculated for each trip as the difference in the mean error estimated for KF and LS models divided by the mean error of the LS model.</p>†<p>N: Number of locations used to calculate errors in locations estimated from LS and KF models.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "locations", "squares", "kalman", "filtered", "harbour"], "article_id"=>969109, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Errors_in_locations_estimated_from_models_fit_to_Least_Squares_LS_and_Kalman_filtered_KF_data_for_all_harbour_seal_trips_/969109", "title"=>"Errors in locations estimated from models fit to Least Squares (LS) and Kalman filtered (KF) data for all harbour seal trips.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429098"], "description"=>"<p>Estimated locations (circles) and tracks (lines) of fin whale #89969 obtained from fitting a switching state-space model to Least Squares (LS) (black) and full Kalman filtered (KF) (red) data. The 95% probability ellipses of locations derived from the LS-based model are shown in green. A. Complete tracks showing the increase in track length resulting from the application of the KF algorithm (red). B, C. Detail of the tracks showing the majority of KF locations within the 95% probability ellipses of LS locations.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "tracks", "ls", "kf", "modelled"], "article_id"=>969108, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.g007", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fin_whale_80704_tracks_obtained_from_LS_black_and_KF_modelled_red_locations_/969108", "title"=>"Fin whale #80704 tracks obtained from LS (black) and KF modelled (red) locations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429093"], "description"=>"<p>Estimated locations (circles) and tracks (lines) of fin whale #89969 obtained from fitting a switching state-space model to Least Squares (LS) (black) and the full Kalman filtered (KF) (red) data. The 95% probability ellipses of locations derived from the LS-based model are shown in green. A. Complete tracks showing the increase in track length resulting from the application of the KF algorithm (red). B, C, D. Detail of the tracks showing the majority of KF locations within the 95% probability ellipses of LS locations.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "tracks", "ls", "kf", "modelled"], "article_id"=>969103, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fin_whale_89969_tracks_obtained_from_LS_black_and_KF_modelled_red_locations_/969103", "title"=>"Fin whale #89969 tracks obtained from LS (black) and KF modelled (red) locations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429089"], "description"=>"<p>Relationship between mean errors (±SD shown as vertical bars) in locations estimated from state-space models fit to Least Squares (LS) (black) and Kalman filtered (KF) (red) data per harbour seal trip and quality of Argos telemetry data used to fit the models: A–B. Number of locations. C–D. Time step (h) between locations. E–F. Proportion of locations of LC 0-B. Different trips from the same seal have the same symbol.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "locations", "ls", "kf", "argos"], "article_id"=>969099, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.g003", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trip_averaged_error_in_locations_estimated_from_LS_and_KF_models_relative_to_Argos_data_quality_/969099", "title"=>"Trip-averaged error in locations estimated from LS and KF models relative to Argos data quality.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429088"], "description"=>"<p>Estimated locations (circles) and tracks (lines) of harbour seals obtained from fitting state-space models to Least Squares (LS) (black) and Kalman filtered (KF) (red) data, in relation to the “true” GPS positions and track (yellow). A. Example of a trip with higher quality of Argos data: trip 7 of harbour seal #43871. B. Example of a trip with lower quality of Argos data: trip 22 of harbour seal #43844.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "tracks", "gps", "ls", "kf", "modelled"], "article_id"=>969098, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Harbour_seal_tracks_obtained_from_GPS_yellow_LS_black_and_KF_modelled_red_locations_/969098", "title"=>"Harbour seal tracks obtained from GPS (yellow), LS (black) and KF modelled (red) locations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429101", "https://ndownloader.figshare.com/files/1429102", "https://ndownloader.figshare.com/files/1429103"], "description"=>"<div><p>Argos recently implemented a new algorithm to calculate locations of satellite-tracked animals that uses a Kalman filter (KF). The KF algorithm is reported to increase the number and accuracy of estimated positions over the traditional Least Squares (LS) algorithm, with potential advantages to the application of state-space methods to model animal movement data. We tested the performance of two Bayesian state-space models (SSMs) fitted to satellite tracking data processed with KF algorithm. Tracks from 7 harbour seals (<i>Phoca vitulina</i>) tagged with ARGOS satellite transmitters equipped with Fastloc GPS loggers were used to calculate the error of locations estimated from SSMs fitted to KF and LS data, by comparing those to “true” GPS locations. Data on 6 fin whales (<i>Balaenoptera physalus</i>) were used to investigate consistency in movement parameters, location and behavioural states estimated by switching state-space models (SSSM) fitted to data derived from KF and LS methods. The model fit to KF locations improved the accuracy of seal trips by 27% over the LS model. 82% of locations predicted from the KF model and 73% of locations from the LS model were <5 km from the corresponding interpolated GPS position. Uncertainty in KF model estimates (5.6±5.6 km) was nearly half that of LS estimates (11.6±8.4 km). Accuracy of KF and LS modelled locations was sensitive to precision but not to observation frequency or temporal resolution of raw Argos data. On average, 88% of whale locations estimated by KF models fell within the 95% probability ellipse of paired locations from LS models. Precision of KF locations for whales was generally higher. Whales’ behavioural mode inferred by KF models matched the classification from LS models in 94% of the cases. State-space models fit to KF data can improve spatial accuracy of location estimates over LS models and produce equally reliable behavioural estimates.</p></div>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "bayesian", "state-space", "argos", "telemetry", "locations", "processed", "kalman"], "article_id"=>969111, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0092277.s001", "https://dx.doi.org/10.1371/journal.pone.0092277.s002", "https://dx.doi.org/10.1371/journal.pone.0092277.s003"], "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assessing_Performance_of_Bayesian_State_Space_Models_Fit_to_Argos_Satellite_Telemetry_Locations_Processed_with_Kalman_Filtering_/969111", "title"=>"Assessing Performance of Bayesian State-Space Models Fit to Argos Satellite Telemetry Locations Processed with Kalman Filtering", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-20 04:07:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1429100"], "description"=>"<p>The matrix shows the number of fin whale locations classified in each behavioural mode by the LS model that were assigned to each of the behavioural modes by the KF model.</p><p>*ARS Area restricted search.</p>", "links"=>[], "tags"=>["ecology", "Behavioral ecology", "Spatial and landscape ecology", "Marine biology", "Marine monitoring", "Zoology", "Animal behavior", "Mammalogy", "marine and aquatic sciences", "Aquatic environments", "Marine environments", "mathematics", "Applied mathematics", "algorithms", "fin", "behavioural", "modes", "inferred", "squares", "kalman", "filtered"], "article_id"=>969110, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Mónica A. Silva", "Ian Jonsen", "Deborah J. F. Russell", "Rui Prieto", "Dave Thompson", "Mark F. Baumgartner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092277.t002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Agreement_between_fin_whale_behavioural_modes_inferred_by_models_fit_to_Least_Squares_LS_and_Kalman_filtered_KF_data_/969110", "title"=>"Agreement between fin whale behavioural modes inferred by models fit to Least Squares (LS) and Kalman filtered (KF) data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-20 04:07:18"}

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Relative Metric

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