Habitat-based Marine Mammal Density Models for the U.S. East Coast

Model History for North Atlantic right whale (Eubalaena glacialis)

These files are © 2015-2022 by the Duke University Marine Geospatial Ecology Laboratory 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 - 2021-11-22

In this update, the density surfaces remain unchanged from version 11, but we have added uncertainty surfaces to go with them. Section 5 of Roberts et al. (2021) gives complete details of how uncertainty was derived. As discussed there, the density surfaces represent means for each month averaged over an era, either 2003-2009, 2010-2018, or 2003-2018. The uncertainty surfaces estimate how much density is likely to vary from the mean if a random year was selected from that era, accounting for the estimated statistical error in model parameter estimates and, when possible, the interannual variability in the model covariates over the era. The uncertainty surfaces include standard error (see Roberts et al. 2021 for the specific definition), the coefficient of variation, and the lower (5%) and upper (95%) limits of a 90% confidence interval. These are similar to what we provided with the model up through version 8, but now account for interannual variability. (Version 8 and prior only accounted for the estimated statistical error in model parameter estimates.)

Documentation

Name: 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. (2020)
Citation: Roberts JJ, Schick RS, Halpin PN (2020) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2018-2020 (Option Year 3). Document version 1.4. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC

Name: Roberts et al. (2021)
Citation: Roberts JJ, Schick RS, Halpin PN (2021) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2020 (Option Year 4). Document version 2.2. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC

Version 11 - 2021-02-27

This was a minor update to version 10, undertaken in response to a request from the Massachusetts Division of Marine Fisheries that we reexamine the problem of how best to estimate abundance in Cape Cod Bay for the month of December. We prepared a new estimate based on all surveys conducted by the Center for Coastal Studies during the month of December from 2003-2020. The only predictions that changed during this update were for grid cells of Cape Cod Bay in the month of December. For more information about this, please see Section 4 of Roberts et al. (2021) and the Appendix of that report.

Documentation

Name: 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. (2020)
Citation: Roberts JJ, Schick RS, Halpin PN (2020) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2018-2020 (Option Year 3). Document version 1.4. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC

Name: Roberts et al. (2021)
Citation: Roberts JJ, Schick RS, Halpin PN (2021) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2020 (Option Year 4). Document version 2.1. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC

Version 10 - 2020-10-13

This was a minor update to version 9, undertaken after NOAA NEFSC (B. Shank) reported implausibly high densities in spring months in the vicinity of Massachusetts Bay. To correct this problem we introduced additional survey data collected by NEFSC in spring of 2019, fixed a model term that caused an unrealistic extrapolation into Massachusetts Bay and refitted the "Spring" model in the "North of Nantucket Shoals" region. This fixed the problem in spring months around Massachusetts Bay, while leaving the rest of the Gulf of Maine region essentially the same as version 9. The additional data included additional effort and sightings in the "Hatteras Island to Nantucket Shoals" region, so we refitted that model as well, resulting in slightly higher predictions south of Nantucket. Predictions south of Hatteras Island are the same as version 9. For more details about this update, please see Section 3 of Roberts et al. (2021).

Documentation

Name: 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. (2020)
Citation: Roberts JJ, Schick RS, Halpin PN (2020) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2018-2020 (Option Year 3). Document version 1.4. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC

Name: Roberts et al. (2021)
Citation: Roberts JJ, Schick RS, Halpin PN (2021) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2020 (Option Year 4). Document version 2.1. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC

Version 9 - 2020-05-06

This was a substantial update over version 8. We extended the aggregate database of surveys to extend up through early 2019 (vs. through 2016 in verison 8). The additional surveys contributed by collaborators included: NOAA NEFSC and SEFSC AMAPPS aerial and shipboard from 2016, 2017, and spring 2019; NEFSC pre-AMAPPS HB-07-09 cruise; NEFSC NARWSS for 2017 through spring 2019; southeast U.S. right whale EWS surveys from 2016/17, 2017/18, and 2018/19; VAMSC Navy surveys for 2016-2017; UNCW Navy surveys 2017; HDR Navy surveys for 2018; NYS-DEC/TetraTech NYBWM Years 1 and 2 surveys (2017-2018); New England Aquarium NLPSC 2011-2015 and MMS-WEA 2017-2018 aerial surveys. We shifted the start date of the model forward to 2003 (vs. 1998 in version 8), to make it more recent and to better equalize survey coverage between the north and south. We increased the spatial resolution to 5 km. At NOAA's request, we adjusted the study area to extend farther inshore in certain bays and estuaries, to facilitate better use of the model in NOAA's right whale take reduction decision support tool. We reformulated and refitted all detection functions and regional spatial models. We applied new availability bias corrections formulated using the Laake et al. (1997) estimator; the corrections accounted for survey altitude and speed, regional whale dive behavior, and, where possible, whale group size and composition. We summarized results into two eras, 2003-2009 and 2010-2018, reflecting the apparant major shift in right whale distributions around 2010. For comparison, we also summarized results in to a third era that spanned the entire period 2003-2018. We documented the overall model in a report to the U.S. Navy (Roberts et al. 2020) in summer 2020 and released it for public use in collaboration with NOAA Fisheries. The Navy Marine Species Density Database (NMSDD) was not updated at this time; the Navy will take delivery of the model in Feburary 2022 as scheduled.

Documentation

Name: 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. (2020)
Citation: Roberts JJ, Schick RS, Halpin PN (2020) Final Project Report: Marine Species Density Data Gap Assessments and Update for the AFTT Study Area, 2018-2020 (Option Year 3). Document version 1.4. Report prepared for Naval Facilities Engineering Command, Atlantic by the Duke University Marine Geospatial Ecology Lab, Durham, NC

Version 8 - 2019-03-26

Updated density predictions for Cape Cod Bay for January-May with estimates from Ganley et al. (2019). Adjusted subregion definitions and model formulations to eliminate edge effects. Otherwise this version is identical to version 7. Model released in collaboration with NOAA Fisheries following the April 2019 ALWTRT meeting.

Documentation

Name: 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

Name: Roberts et al. (2019)
Citation: Roberts JJ, Schick RS, Halpin PN (2019) North Atlantic right whale density models: Brief Overview for the April 2019 ALWTRT Meeting. Presented 23 April 2019 in Providence, RI.

Version 7 - 2017-09-30

Switched back to four season model with new season and subregion definitions (relative to Roberts et al. 2015). Model released as part of a scheduled update to the U.S. Navy Marine Species Density Database (NMSDD).

Documentation

Name: 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 6 - 2017-06-01 (unreleased)

Began update to Roberts et al. (2015) model. Introduced new surveys from AMAPPS, NARWSS, UNCW, VAMSC, and the SEUS NARW teams. Updated modeling methodology. Switched to a two-season spatial model and adjusted model subregions. Changed aerial g(0) estimates to be based on geographic region, group size, and presence of calves. Refitted detection functions and spatial models from scratch using new and reprocessed covariates.

Version 5.6 - 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 5.4 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).

Documentation

Name: 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 North Atlantic Right Whale (Eubalaena glacialis) for the U.S. East Coast Version 5.6, 2016-04-21, and Supplementary Report. Marine Geospatial Ecology Lab, Duke University, Durham, NC

Version 5.5 - 2015-10-12 (unreleased)

Updated the documentation. No changes to the model.

Version 5.4 - 2015-05-14 (unreleased)

Updated calculation of CVs. Switched density rasters to logarithmic breaks. No changes to the model.

Version 5.3 - 2015-04-06 (unreleased)

Updated the documentation. No changes to the model.

Version 5.2 - 2015-03-06 (unreleased)

Updated the documentation. No changes to the model.

Version 5.1 - 2015-01-20 (unreleased)

Updated the documentation. No changes to the model.

Version 5 - 2015-01-20 (unreleased)

Added additional surveys from UNCW and Virginia Aquarium. Changed winter to four months (Dec-Mar), spring to two (Apr-May), and summer and fall to three (Jun-Aug and Sep-Nov).

Version 4 - 2014-05-28 (unreleased)

Shrunk spring and fall seasons to two months, expanded summer to five. 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.

Version 3 - 2013-05-08 (unreleased)

Figures regenerated with improved label placement. No changes to models.

Version 2 - 2013-04-30 (unreleased)

All four seasons modeled; many improvements implemented, too numerous to list.

Version 1 - 2013-02-20 (unreleased)

Draft model of spring season only, for NOAA internal meetings.

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