A Network Extension of Species Occupancy Models in a Patchy Environment Applied to the Yosemite Toad (Anaxyrus canorus)
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{"title"=>"A Network Extension of Species Occupancy Models in a Patchy Environment Applied to the Yosemite Toad (Anaxyrus canorus)", "type"=>"journal", "authors"=>[{"first_name"=>"Eric L.", "last_name"=>"Berlow", "scopus_author_id"=>"6602671674"}, {"first_name"=>"Roland A.", "last_name"=>"Knapp", "scopus_author_id"=>"7201853267"}, {"first_name"=>"Steven M.", "last_name"=>"Ostoja", "scopus_author_id"=>"30267899300"}, {"first_name"=>"Richard J.", "last_name"=>"Williams", "scopus_author_id"=>"55612751800"}, {"first_name"=>"Heather", "last_name"=>"McKenny", "scopus_author_id"=>"55820569500"}, {"first_name"=>"John R.", "last_name"=>"Matchett", "scopus_author_id"=>"6603189888"}, {"first_name"=>"Qinghua", "last_name"=>"Guo", "scopus_author_id"=>"56390927100"}, {"first_name"=>"Gary M.", "last_name"=>"Fellers", "scopus_author_id"=>"6603917765"}, {"first_name"=>"Patrick", "last_name"=>"Kleeman", "scopus_author_id"=>"6604031642"}, {"first_name"=>"Matthew L.", "last_name"=>"Brooks", "scopus_author_id"=>"7201999426"}, {"first_name"=>"Lucas", "last_name"=>"Joppa", "scopus_author_id"=>"23566616300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84881497360", "doi"=>"10.1371/journal.pone.0072200", "issn"=>"19326203", "pmid"=>"23951296", "scopus"=>"2-s2.0-84881497360", "pui"=>"369566288", "isbn"=>"1932-6203"}, "id"=>"66b72e89-7d4a-34df-8d66-7b6f2b6e0d37", "abstract"=>"A central challenge of conservation biology is using limited data to predict rare species occurrence and identify conservation areas that play a disproportionate role in regional persistence. Where species occupy discrete patches in a landscape, such predictions require data about environmental quality of individual patches and the connectivity among high quality patches. We present a novel extension to species occupancy modeling that blends traditional predictions of individual patch environmental quality with network analysis to estimate connectivity characteristics using limited survey data. We demonstrate this approach using environmental and geospatial attributes to predict observed occupancy patterns of the Yosemite toad (Anaxyrus (= Bufo) canorus) across >2,500 meadows in Yosemite National Park (USA). A. canorus, a Federal Proposed Species, breeds in shallow water associated with meadows. Our generalized linear model (GLM) accurately predicted ~84% of true presence-absence data on a subset of data withheld for testing. The predicted environmental quality of each meadow was iteratively 'boosted' by the quality of neighbors within dispersal distance. We used this park-wide meadow connectivity network to estimate the relative influence of an individual Meadow's 'environmental quality' versus its 'network quality' to predict: a) clusters of high quality breeding meadows potentially linked by dispersal, b) breeding meadows with high environmental quality that are isolated from other such meadows, c) breeding meadows with lower environmental quality where long-term persistence may critically depend on the network neighborhood, and d) breeding meadows with the biggest impact on park-wide breeding patterns. Combined with targeted data on dispersal, genetics, disease, and other potential stressors, these results can guide designation of core conservation areas for A. canorus in Yosemite National Park.", "link"=>"http://www.mendeley.com/research/network-extension-species-occupancy-models-patchy-environment-applied-yosemite-toad-anaxyrus-canorus", "reader_count"=>46, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>17, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>3, "Other"=>6, "Student > Master"=>6, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>17, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>3, "Other"=>6, "Student > Master"=>6, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>16, "Biochemistry, Genetics and Molecular Biology"=>2, "Mathematics"=>1, "Agricultural and Biological Sciences"=>20, "Computer Science"=>2, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>16}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>7, "South Africa"=>2, "Italy"=>1, "United Kingdom"=>1, "Chile"=>1, "Spain"=>1, "Indonesia"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1149761"], "description"=>"<p>a) Watersheds with high mean predicted probability of <i>A</i><i>. canorus</i> breeding (Environmental Model) tend to have low coefficient of variation (CV) in breeding probabilities among meadows within the watershed. b) Watersheds with high mean breeding probability across also show high normalized network improvement in the predicted breeding probabilities due to spatial clustering of ‘intrinsically good’ meadows. ‘Normalized network improvement’ is the proportional increase in Environmental Model predicted probability relative to the maximum improvement possible.</p>", "links"=>[], "tags"=>["patterns"], "article_id"=>769611, "categories"=>["Biological Sciences", "Earth and Environmental Sciences", "Ecology"], "users"=>["Eric L. Berlow", "Roland A. Knapp", "Steven M. Ostoja", "Richard J. Williams", "Heather McKenny", "John R. Matchett", "Qinghua Guo", "Gary M. Fellers", "Patrick Kleeman", "Matthew L. Brooks", "Lucas Joppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072200.g003", "stats"=>{"downloads"=>3, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Watershed_scale_patterns_of_predicted_breeding_/769611", "title"=>"Watershed scale patterns of predicted breeding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-12 02:02:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1149762"], "description"=>"<p>The watersheds (Cal 2.2.2 watershed planning units) are colored by the percent of meadows within the basin that are predicted by the Network Boosted GLM model to have breeding. The symbols are centroids for all 2,558 contiguous meadows in the park. Pink and/or red symbols indicate a meadow with observed <i>A</i><i>. canorus</i> breeding at least once between 1992–2010. Blue symbols were visited at least once with no <i>A</i><i>. canorus</i> detected. Small black dots are meadows that have not been visited. Solid read symbols are meadows with breeding that are in 90<sup>th</sup> percentile of impact on park-wide breeding probability if deleted. Note that meadows with high deletion impact are not in the watersheds with highest proportion of ‘good’ meadows.</p>", "links"=>[], "tags"=>["meadows", "watersheds", "breeding", "yosemite"], "article_id"=>769612, "categories"=>["Biological Sciences", "Earth and Environmental Sciences", "Ecology"], "users"=>["Eric L. Berlow", "Roland A. Knapp", "Steven M. Ostoja", "Richard J. Williams", "Heather McKenny", "John R. Matchett", "Qinghua Guo", "Gary M. Fellers", "Patrick Kleeman", "Matthew L. Brooks", "Lucas Joppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072200.g004", "stats"=>{"downloads"=>3, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Observed_and_predicted_distribution_of_meadows_and_watersheds_with_A_canorus_breeding_in_Yosemite_National_Park_/769612", "title"=>"Observed and predicted distribution of meadows and watersheds with <i>A</i><i>. canorus</i> breeding in Yosemite National Park.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-12 02:02:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1149759"], "description"=>"<p>a) The distribution of probabilities for the three classes of data for the Environmental Model (see Methods: “100subsampleGLM”). Data are combined from all surveys from 1996–2010. b) ROC plot for the training and test data. The red line shows the fit of the model to the training data, while the blue shows the fit relative to the test data. The curves represent those drawn from the average probabilities across 100 models.</p>", "links"=>[], "tags"=>[], "article_id"=>769609, "categories"=>["Biological Sciences", "Earth and Environmental Sciences", "Ecology"], "users"=>["Eric L. Berlow", "Roland A. Knapp", "Steven M. Ostoja", "Richard J. Williams", "Heather McKenny", "John R. Matchett", "Qinghua Guo", "Gary M. Fellers", "Patrick Kleeman", "Matthew L. Brooks", "Lucas Joppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072200.g001", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_of_the_8220_Environmental_Model_8221_/769609", "title"=>"Performance of the “Environmental Model.”", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-12 02:02:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1149760"], "description"=>"<p>a) Normalized Network Improved breeding probabilities ((Network Boosted probability – Environmental Model probability) / (1 – Environmental Model probability)) for each meadow as a function of the mean Environmental Model probability. Symbol colors represent field survey results (Breeding detected (red), Breeding not detected (blue), and Meadow not visited (black). b-c) Total Influence (G<sub><i>i</i></sub>) of meadow deletion (the decrease in park-wide breeding probability summed across all meadows after deleting that meadow from the network) as a function of the Environmental Model and the Network-Boosted GLM probabilities. Horizontal dotted lines indicate the 90<sup>th</sup> percentile of meadow deletion impact, and solid red symbols are the known breeding meadows within that 90<sup>th</sup> percentile. Vertical dotted lines in all panels represent the threshold probability that maximizes both true positives and true negatives predicted by the model.</p>", "links"=>[], "tags"=>["intrinsic", "meadow", "spatial"], "article_id"=>769610, "categories"=>["Biological Sciences", "Earth and Environmental Sciences", "Ecology"], "users"=>["Eric L. Berlow", "Roland A. Knapp", "Steven M. Ostoja", "Richard J. Williams", "Heather McKenny", "John R. Matchett", "Qinghua Guo", "Gary M. Fellers", "Patrick Kleeman", "Matthew L. Brooks", "Lucas Joppa"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0072200.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Disentangling_intrinsic_meadow_environmental_quality_from_its_spatial_network_quality_with_respect_to_predicted_A_canorus_breeding_/769610", "title"=>"Disentangling intrinsic meadow ‘environmental quality’ from its spatial ‘network quality’ with respect to predicted <i>A</i><i>. canorus</i> breeding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-12 02:02:26"}

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Zoology", "average_usage"=>[294, 473, 591, 693, 788, 883, 972, 1054, 1140, 1222, 1299, 1381, 1446]}, {"subject_area"=>"/Earth sciences", "average_usage"=>[296, 488, 620, 717, 828, 938, 1038, 1130, 1230, 1328, 1414, 1502, 1592]}, {"subject_area"=>"/Ecology and environmental sciences/Aquatic environments", "average_usage"=>[276, 480, 624, 713, 810, 927, 1024, 1130, 1221, 1318, 1422, 1506, 1587]}, {"subject_area"=>"/Ecology and environmental sciences/Conservation science", "average_usage"=>[390, 618, 766, 904, 1030, 1153, 1268, 1391, 1487, 1591, 1685, 1767, 1865]}, {"subject_area"=>"/Ecology and environmental sciences/Species colonization", "average_usage"=>[251, 396, 508, 594, 692, 774, 847, 918, 1000, 1061, 1113, 1187, 1246]}]}
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