Final Technical Report: - Southwest Fisheries Science Center - NOAA

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Table 10 cont. Comparison of the simple and complex encounter rate GAMs for the ETP. Guild Model Type gam.method Spline gamma Total EDF sum(abs(1-R)) Explained Deviance ASPE Cuvier's Beaked Whale Simple perf.magic cs 1.000 7.027 2.023 0.056 0.005 Complex perf.magic ts 1.000 8.973 1.742 0.057 0.005 Blue Whale Simple perf.magic cs 1.400 24.174 4.092 0.215 0.005 Complex NA NA NA NA NA NA NA Bryde's Whale Simple perf.magic ts 1.000 10.284 1.697 0.058 0.012 Complex NA NA NA NA NA NA NA Short-finned Pilot Whale Simple perf.magic cs 1.000 16.160 1.715 0.061 0.014 Complex outer ts 1.400 57.162 1.625 0.086 0.014 Dwarf Sperm Whale Simple perf.outer cs 1.400 26.920 1.273 0.342 0.005 Complex outer cs 1.000 61.997 0.646 0.388 0.005 Mesoplodon spp. Simple perf.outer cs 1.000 52.296 1.736 0.140 0.005 Complex NA NA NA NA NA NA NA Small Beaked Whale Simple perf.magic cs 1.000 12.934 1.276 0.091 0.012 Complex perf.outer cs 1.000 44.111 1.152 0.109 0.012 52
Table 11. Comparison of the simple and complex group size GAMs for the ETP. All models were built using the gam algorithm in the R package mgcv. The term gam.method refers to the numerical method used to optimize the smoothing parameter estimation criterion for the gam. Splines were either cubic regression splines with shrinkage (cs) or thin plate regression splines with shrinkage (ts). The gamma parameter determines the penalty for model complexity, with larger values of gamma resulting in greater penalty. Also shown are the total effective degrees of freedom (EDF), the sum of the absolute value of the deviance in the ratio of observed to predicted number of sightings, the explained deviance, and the average squared prediction error (ASPE) for the best model re-fit using all data from 1986-2006 (or 1998-2006 for offshore spotted dolphins). If a single model outperformed all others, the corresponding elements of the table show "NA" for the type of model that was not considered any further. Model Total sum(abs(1- Guild Type gam.method Spline gamma EDF R)) Explained Deviance ASPE Offshore spotted dolphin Simple magic cs 1.400 3.830 1.663 0.038 6734.449 Complex NA NA NA NA NA NA NA Eastern spinner dolphin Simple magic ts 1.400 13.222 2.161 0.105 12863.707 Complex mgcv cs 1.000 21.621 1.992 0.150 12517.964 Whitebelly spinner dolphin Simple magic ts 1.000 1.783 0.776 0.083 41435.168 Complex NA NA NA NA NA NA NA Striped dolphin Simple magic ts 1.400 12.641 0.543 0.089 2898.201 Complex mgcv ts 1.000 17.934 0.473 0.098 2890.072 Rough-toothed dolphin Simple magic ts 1.400 6.789 1.672 0.148 114.062 Complex NA NA NA NA NA NA NA Short-beaked common dolphin Simple magic cs 1.400 10.974 1.627 0.138 83237.681 Complex magic ts 1.000 21.745 1.094 0.215 77358.863 Bottlenose dolphin Simple magic ts 1.400 10.162 1.183 0.060 12433.442 Complex mgcv cs 1.000 27.789 1.292 0.118 12461.770 Risso's dolphin Simple magic ts 1.400 5.031 0.570 0.096 353.787 Complex magic cs 1.000 20.570 0.294 0.208 304.655 53
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U N I R A P E D T T E M D S E N TA
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C O L A N IO T A N U N C I EA .S. D
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This report was prepared under cont
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Table of Contents Acronyms and Abbr
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C.1 Journal Publications ..........
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Figure 18. Encounter rate models bu
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List of Tables Table 1. Summary of
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Appendix B, Table B-6. Summary of m
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Acknowledgements This project was f
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of these choices as possible and us
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Although our models include most of
Page 24 and 25: 2.0 Background The Navy and other m
Page 26 and 27: comparison is based on a separate s
Page 28 and 29: Figure 1. Transects (green lines) s
Page 30 and 31: used to evaluate the ability of sum
Page 32 and 33: 3.1.5 Mid-trophic Sampling with Net
Page 34 and 35: variable. Interpolated maps of the
Page 36 and 37: Table 2. Variogram model results. A
Page 38 and 39: “number of individuals” as the
Page 40 and 41: Encounter Rate and Group Size Model
Page 42 and 43: were built separately for each of t
Page 44 and 45: Expanding models to the entire U.S.
Page 46 and 47: Table 4. Summary of the weighted ef
Page 48 and 49: Consistent with Barlow and Forney (
Page 50 and 51: incorporation of geographic coordin
Page 52 and 53: overwhelming majority of “Bryde
Page 54 and 55: the genera Ziphius and Mesoplodon.
Page 56 and 57: Table 7. Geographically stratified
Page 58 and 59: above, and the data themselves, are
Page 60 and 61: (hereafter “summer”). SWFSC has
Page 62 and 63: avoid these problems, we decided to
Page 64 and 65: Figure 9. Thermocline depth (m) obs
Page 66 and 67: Attempts to adjust search parameter
Page 68 and 69: CAMMS 1991 PODS 1993 ORCAWALE 1996
Page 70 and 71: 4.2 Modeling Framework : GLM and GA
Page 72 and 73: 4.2.4 Conclusions Regardings Modeli
Page 76 and 77: Table 11 cont. Comparison of the si
Page 78 and 79: Figure 15. The transect lines used
Page 80 and 81: A) Striped dolphin 10 km B) Short-b
Page 82 and 83: dependent. For example, the number
Page 84 and 85: Figure 19. Predicted average densit
Page 86 and 87: ecosystem, eastern spinner dolphins
Page 88 and 89: Table 13. Variables selected for mo
Page 90 and 91: Table 14. Starting and final AIC va
Page 92 and 93: Table 17. Ratios of observed to pre
Page 94 and 95: species represented in the acoustic
Page 96 and 97: 0.29 (Risso’s dolphin) to 3.20 (n
Page 98 and 99: Figure 25. Sample 2005 validation p
Page 100 and 101: Table 18. (continued) 1991 1993 Nor
Page 102 and 103: Blue whales had the greatest deviat
Page 104 and 105: Table 20. Abundance (number of anim
Page 106 and 107: Table 22. Proportion of deviance ex
Page 108 and 109: Figure 27. Average density (AveDens
Page 110 and 111: Table 23. Effective degrees of free
Page 112 and 113: We attempted to build encounter rat
Page 114 and 115: 5.0 Conclusion The field of predict
Page 116 and 117: 6.0 Transition Plan The models of c
Page 118 and 119: needed to ensure that the SDSS rema
Page 120 and 121: Administrative Report LJ-07-02. NOA
Page 122 and 123: Forney KA, Barlow J (1993) Prelimin
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Redfern JV, Barlow J, Ballance LT,
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Appendix A: Detailed Model Results
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Table A-1 (continued) Blue whale 19
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Figure A-1a. Striped dolphin 108
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Figure A-1c. Risso’s dolphin 110
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Figure A-1e. Northern right whale d
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Figure A-1g. Sperm whale 114
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Figure A-1i. Blue whale 116
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Figure A-1k. Baird’s beaked whale
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Figure A-2. Predicted average densi
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Figure A-2b. Short-beaked common do
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Figure A-2d. Pacific white-sided do
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Figure A-2f. Dall’s porpoise 126
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Figure A-2h. Fin whale 128
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Figure A-2j. Humpback whale 130
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Figure A-2l. Small beaked whales 13
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Table B-2. Summary of model validat
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Table B-10. Summary of model valida
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Figure B-1. Predicted yearly and av
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Figure B-1. b) Eastern spinner dolp
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Figure B-1. c) Whitebelly spinner d
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Figure B-1. d) Striped dolphin 168
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Figure B-1. e) Rough-toothed dolphi
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Figure B-1. f) Short-beaked common
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Figure B-1. g) Bottlenose dolphin 1
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Figure B-1. h) Risso’s dolphin 17
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Figure B-1. i) Cuvier’s beaked wh
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Figure B-1. j) Blue whale 180
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Figure B-1. k) Bryde’s whale 182
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Figure B-1. l) Short-finned pilot w
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Figure B-1. m) Dwarf sperm whale 18
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Figure B-1. n) Mesoplodon beaked wh
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Figure B-1. o) Small beaked whales
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Figure B-2. Predicted average densi
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Figure B-2. (cont.) c) Whitebelly s
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Figure B-2. (cont.) g) Bottlenose d
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Figure B-2. (cont.) k) Bryde’s wh
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Figure B-2. (cont.) o) Small beaked
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Ferguson MC (2005) Cetacean Populat
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Barlow J, Kahru M, Mitchell BG (In
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Memorandum NMFS-SWFSC-374, U.S. Dep
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