Duke Models for the U.S. East Coast
Model History for Humpback whale (Megaptera novaeangliae)
These files are © 2015-2023 Marine Geospatial Ecology Lab and licensed under a Creative Commons Attribution 4.0 International License. If you use them in a scientific publication or technical report, we kindly request that you cite the documentation listed for the model you use.
Version 11.1 - 2023-05-27
Completed the supplementary report documenting the details of this model. The model itself was not changed.
DocumentationName: Roberts et al. (2016) Citation: Roberts JJ, Best BD, Mannocci L, Fujioka E, Halpin PN, Palka DL, Garrison LP, Mullin KD, Cole TVN, Khan CB, McLellan WM, Pabst DA, Lockhart GG (2016) Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico. Scientific Reports 6: 22615. doi: 10.1038/srep22615 Name: Roberts et al. (2023) Citation: Roberts JJ, Yack TM, Halpin PN (2023) Marine mammal density models for the U.S. Navy Atlantic Fleet Training and Testing (AFTT) study area for the Phase IV Navy Marine Species Density Database (NMSDD). Document version 1.3. Report prepared for Naval Facilities Engineering Systems Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC Name: Roberts et al. (2022) Citation: Roberts JJ, Yack TM, Canadas A, Fujioka E, Halpin PN, Barco SG, Boisseau O, Chavez-Rosales S, Cole TVN, Cotter MP, Cummings EW, Davis GE, DiGiovanni Jr. RA, Garrison LP, Gowan TA, Jackson KA, Kenney RD, Khan CB, Lockhart GG, Lomac-MacNair KS, McAlarney RJ, McLellan WA, Mullin KD, Nowacek DP, O'Brien O, Pabst DA, Palka DL, Quintana-Rizzo E, Redfern JV, Rickard ME, White M, Whitt AD, Zoidis AM (2022) Density Model for Humpback Whale (Megaptera novaeangliae) for the U.S. East Coast, Version 11.1, 2023-05-27, and Supplementary Report. Marine Geospatial Ecology Laboratory, Duke University, Durham, NC | |
Version 11 - 2022-06-20
This model is a major update over the prior version, with substantial additional data, improved statistical methods, and an increased spatial resolution. It was released as part of the final delivery of the U.S. Navy Marine Species Density Database (NMSDD) for the Atlantic Fleet Testing and Training (AFTT) Phase IV Environmental Impact Statement. Several new collaborators joined and contributed survey data: New York State Department of Environmental Conservation, TetraTech, HDR, and Marine Conservation Research. We incorporated additional surveys from all continuing and new collaborators through the end of 2020. (Because some environmental covariates were only available through 2019, certain models only extend through 2019.) We increased the spatial resolution to 5 km and, at NOAA's request, we extended the model further inshore from New York through Maine. We reformulated and refitted all detection functions and spatial models. We updated all environmental covariates to newer products, when available, and added several covariates to the set of candidates. For models that incorporated dynamic covariates, we estimated model uncertainty using a new method that accounts for both model parameter error and temporal variability.
DocumentationName: Roberts et al. (2016a) Citation: Roberts JJ, Best BD, Mannocci L, Fujioka E, Halpin PN, Palka DL, Garrison LP, Mullin KD, Cole TVN, Khan CB, McLellan WM, Pabst DA, Lockhart GG (2016) Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico. Scientific Reports 6: 22615. doi: 10.1038/srep22615 | |
Version 10 - 2017-06-01
Began update to Roberts et al. (2015) model. Introduced new surveys from AMAPPS, NARWSS, UNCW, VAMSC, and the SEUS NARW teams. Updated modeling methodology. Refitted detection functions and spatial models from scratch using new and reprocessed covariates. Model released as part of a scheduled update to the U.S. Navy Marine Species Density Database (NMSDD).
DocumentationName: Roberts et al. (2016a) Citation: Roberts JJ, Best BD, Mannocci L, Fujioka E, Halpin PN, Palka DL, Garrison LP, Mullin KD, Cole TVN, Khan CB, McLellan WM, Pabst DA, Lockhart GG (2016) Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico. Scientific Reports 6: 22615. doi: 10.1038/srep22615 Name: Roberts et al. (2016b) Citation: Roberts JJ, Mannocci L, Halpin PN (2016) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2015-2016 (Base Year). Document version 1.0. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC Name: Roberts et al. (2017) Citation: Roberts JJ, Mannocci L, Halpin PN (2017) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2016-2017 (Opt. Year 1). Document version 1.4. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC | |
Version 9.4 - 2016-04-21
Switched calculation of monthly 5% and 95% confidence interval rasters to the method used to produce the year-round rasters. (We intended this to happen in version 9.2 but I did not implement it properly.) Updated the monthly CV rasters to have value 0 where we assumed the species was absent, consistent with the year-round CV raster. No changes to the other (non-zero) CV values, the mean abundance rasters, or the model itself. Model files released as supplementary information to Roberts et al. (2016).
DocumentationName: Roberts et al. (2016) Citation: Roberts JJ, Best BD, Mannocci L, Fujioka E, Halpin PN, Palka DL, Garrison LP, Mullin KD, Cole TVN, Khan CB, McLellan WM, Pabst DA, Lockhart GG (2016) Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico. Scientific Reports 6: 22615. doi: 10.1038/srep22615 Name: Density Model Supplementary Report Citation: Roberts JJ, Best BD, Mannocci L, Fujioka E, Halpin PN, Palka DL, Garrison LP, Mullin KD, Cole TVN, Khan CB, McLellan WM, Pabst DA, Lockhart GG (2016) Density Model for Humpback Whale (Megaptera novaeangliae) for the U.S. East Coast Version 9.4, 2016-04-21, and Supplementary Report. Marine Geospatial Ecology Lab, Duke University, Durham, NC | |
Version 9.3 - 2015-09-26 (unreleased)
Updated the documentation. No changes to the model.
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Version 9.2 - 2015-05-14 (unreleased)
Updated calculation of CVs. Switched density rasters to logarithmic breaks. No changes to the model.
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Version 9.1 - 2015-03-05 (unreleased)
Updated the documentation. No changes to the model.
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Version 9 - 2014-12-03 (unreleased)
Fixed bug that applied the wrong detection function to segments NE_narwss_1999_widgeon_hapo dataset. Refitted models. Updated documentation.
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Version 8 - 2014-11-11 (unreleased)
Reconfigured detection hierarchy and adjusted NARWSS detection functions based on additional information from Tim Cole. Removed CumVGPM180 predictor. Updated documentation.
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Version 7 - 2014-10-15 (unreleased)
Added Palka (2006) survey-specific g(0) estimates. Removed distance to eddy predictors and wind speed predictor from all models; they were not ecologically justified. Fixed missing pixels in several climatological predictors, which led to not all segments being utilized. Eliminated Cape Cod Bay subregion.
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Version 6 - 2014-09-02 (unreleased)
Added surveys: NJ-DEP, Virginia Aquarium, NARWSS 2013, UNCW 2013. Extended study area up Scotian Shelf. Added SEAPODYM predictors. Switched to mgcv estimation of Tweedie p parameter (family=tw()).
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Version 5 - 2014-05-20 (unreleased)
Fixed bug in temporal variability plots. Density models unchanged.
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Version 4 - 2014-05-14 (unreleased)
Added discussion of acoustic monitoring studies to text. Eliminated accidentally-included off-effort sighting at Cape Lookout (2006-04-20 14:14:00). Refitted summer model.
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Version 3 - 2014-03-01 (unreleased)
Switched from four seasonal models to two. Reformulated density model using a Horvitz-Thompson estimator. Eliminated GAM for group size (consequence of above). Added group size as a candidate covariate in detection functions (benefit of above). Added survey ID as a candidate covariate in NOAA NARWSS detection functions. Took more care in selecting right-truncation distances. Fitted models with contemporaneous predictors, for comparison to climatological. Switched SST and SST fronts predictors from NOAA Pathfinder to GHRSST CMC0.2deg L4. Changed SST fronts algorithm to use Canny operator instead of Cayula-Cornillon. Switched winds predictors from SCOW to CCMP (SCOW only gives climatol. estimates.) Added DistToEddy predictors, based on Chelton et al. (2011) eddy database. Added cumulative VGPM predictors, summing productivity for 45, 90, and 180 days. Added North Atlantic Oscillation (NAO) predictor; included 3 and 6 month lags. Transformed predictors more carefully, to better minimize leverage of outliers. Implemented hybrid hierarchical-forward / exhaustive model selection procedure. Model selection procedure better avoids concurvity between predictors. Allowed GAMs to select between multiple formulations of dynamic predictors. Adjusted land mask to eliminate additional estuaries and hard-to-predict cells.
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Version 2 - 2013-05-08 (unreleased)
Figures regenerated with improved label placement.
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Version 1 - 2013-05-03 (unreleased)
Initial version.
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