NOAA Technical Memorandum NMFS-AFSC-84


Observations of Harbor Porpoise 

in the Vicinity of Acoustic Alarms 

on a Set Gill Net 

by 

J. Laake, D. Rugh, and L. Baraff

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration 

National Marine Fisheries Service 

Alaska Fisheries Science Center 

January 1998 
NOAA Technical Memorandum NMFS 

The National Marine Fisheries Service’s Alaska Fisheries Science Center 

uses the NOAA Technical Memorandum series to issue informal scientific and 

technical publications when complete formal review and editorial processing 

are not appropriate or feasible. Documents within this series reflect sound 

professional work and may be referenced in the formal scientific and technical 

literature. 

The NMFS-AFSC Technical Memorandum series of the Alaska Fisheries 

Science Center continues the NMFS-F/NWC series established in 1970 by the 

Northwest Fisheries Center. The new NMFS-NWFSC series will be used by 

the Northwest Fisheries Science Center. 

This document should be cited as follows: 

Laake, J., D. Rugh, and L. Baraff. 1998. Observations of harbor 

porpoise in the vicinity of acoustic alarms on a set gill net. U. S. Dep. 

Commer., NOAA Tech. Memo. NMFS-AFSC-84,40 p. 

Reference in this document to trade names does not imply endorsement by 

the National Marine Fisheries Service, NOAA. 
Technical Memorandum NMFS-AFSC-84

Observations of Harbor Porpoise 

in the Vicinity of Acoustic Alarms 

on a Set Gill Net 

by J. Laake, D. Rugh, and L. Baraff

National Marine Mammal Laboratory 

Alaska Fisheries Science Center 

7600 Sand Point Way N.E., BIN C-15700 

Seattle, WA 98115-0070 

U.S. DEPARTMENT OF COMMERCE 

William M. Daley, Secretary 

National Oceanic and Atmospheric Administration 

D. James Baker, Under Secretary and Administrator

National Marine Fisheries Service 

Rolland A. Schmitten, Assistant Administrator for Fisheries 

January 1998 
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ABSTRACT 

Large and small-scale fishery experiments have demonstrated that attaching acoustic 

devices (pingers) on gill nets reduces harbor porpoise (Phocoenaphocoena) entanglement and 

mortality. However, the mechanism for mortality reduction is unknown. We conducted shorebased observations of a set gill net that was alternately set with and without alarms for 2- to 5-day 

periods during 27 days between 11 July - 6 August 1996. When the acoustic alarms were 

attached to the net, harbor porpoise were displaced by an acoustic buffer with a radius of at least 

125 m around the net (P <O.Ol), which demonstrated the effectiveness of pingers in reducing 

entanglement. 

iii 
CONTENTS

Analysis 

Results 

Discussion 

Acknowledgments 

Citations 

Figures 

Abstract 

Introduction. 

Methods 

Study Area Description 

Net Array 

Experimental Design/Survey Protocol 

Tables 

iii 

1 

2 

2 

2 

3

 5

 8 

10 

11 

13 

15 

18 

29 

35 

Appendix A - Details of Cliff-height Computation 21 

Appendix B - Field Procedure Details 

Appendix C - Analysis Details 

V 
INTRODUCTION 

Pingers have dramatically reduced incidental harbor porpoise (Phocoena phocoena) 

mortality in experiments conducted with the sink gill net fishery in the Gulf of Maine (Kraus et al. 

1997) and the Makah Tribal set gill net fishery (Gearin et al. 1996) off the coast of Washington 

State. However, the mechanism for mortality reduction is unknown. The report of the Workshop 

on Acoustic Deterrence (Reeves et al. 1996) concludes: 

Although it is clear that the pingers significantly reduced the harbor 

porpoise bycatch in the [Gulf of Maine] experiment, it is not clear why they 

worked. For example, it is not clear whether porpoises were alerted or 

repelled by the sounds made by the pingers; their prey responded by moving 

away from the sounds and the porpoises followed; or other factors were 

involved. 

The workshop recommended conducting “studies of the fine-scale distribution of porpoises in 

areas where pingers are used, to look for signs of displacement and other effects”. 

To address the workshop recommendation, we repeated the work of Gearin et al. (1996) 

to assess the effectiveness of pingers at reducing incidental mortality and included the following 

additional objectives: 1) measure the effects of pingers on the fine-scale distribution of porpoise 

by observing surfacing harbor porpoise in relation to a set gill net that was alternately set with 

pingers (alarmed) and without pingers (unalarmed); and 2) determine signal to noise ratios of the 

pinger frequencies in the region surrounding the net by recording acoustic measurements when 

the net was alarmed and unalarmed. We report here on the study of the effects of pingers on the 

fine-scale distribution of harbor porpoise. 
METHODS 

Study Area Description 

The Spike Rock Fishery Area, seaward of Shi Shi Beach, is within the Olympic Coast 

National Marine Sanctuary in the Pacific Ocean at the northwestern edge of the Olympic National 

Park in Washington State (Fig. 1). Water depths do not exceed 20 m within the study area at 

mean tide levels. During the survey period, 11 July to 6 August, daily differences between low 

and high tides ranged from as little as 1.6 m up to 4.4 m (from -1 .0 m to +3.4 m). 

Observations of the Spike Rock Fishery Area were made from a site on an exposed bluff 

northeast of Shi Shi Beach (48°6.5’N, 124°40.7’W). The observation site was located on the 

Makah Indian Reservation, adjacent to the Olympic National Park. Vegetation at the observation 

site limited the field of view of the Spike Rock Fishery area to 56° (magnetic 202.5° to 259.2° for 

the inshore observer, and 197.2° to 253.5° for the offshore observer; magnetic declination was 

+21.3°). The site altitude, 46.8 m (149 A) above sea level at a 0 m tide, was determined by using 

triangulation with a pair of targets at sea level separated by a known distance (Appendix A). 

Distances based on vertical angles from the horizon or horizontal used the 46.8 m height adjusted 

for tide height at the time of the measurement, which was interpolated between extremes from a 

tide table. 

Net Array 

Four set gill nets (Nos. 10-13) were deployed with net No. 12 and No. 13 (183 m long by 

10 m deep) placed near the south side of the Spike Rock Fishery Area, and net No. 10 and No. 11 

2 
(183 m long by 16 m deep) placed opposite the shore-based observers (Fig. 1, Table 1). The ends 

of each net were marked by orange buoys attached to the cork line. Theodolite bearings to each 

buoy were recorded at low and high tides each day, providing a record of net locations relative to 

porpoise sightings. Daily measurements were used to construct an average position of each net. 

The theodolite (Nikon NT2A) was accurate to 0.006° with a 19 power lens and an optical field of 

view of 1.50°. Vertical readings were determined relative to a precisely leveled bubble; horizontal 

bearings were determined relative to magnetic north. A distinctive notch on Spike Rock, at the 

far end of the survey area, was used to calibrate the horizontal bearings (set at 211°OO’OO”). Buoy 

locations were also determined using a Global Positioning System (GPS), aboard the fishing 

vessel that attended the nets. 

Experimental Design/Survey Protocol 

Eleven pingers, built to the specifications of John Lien (Fullilove 1994) were placed on 

the corkline of each net at 16.6 m intervals to create an acoustic alarm (Gearin et al. 1996). 

Initially we intended to place pingers on one net within each of the two pairs No. 10 - No. 11 and 

No. 12 - No. 13. The pingers were to be rotated between nets within each pair every 2 days. This 

design was followed for the first week of the 1996 study; however, as we collected acoustic 

measurements, it became clear that the lower tonal component (3Hz) of the pings was discernible 

between nets within the same pair (Bowles, unpub. data). Therefore, we modified the original 

design such that both nets in each pair were either alarmed or unalarmed. Inclement weather 

sometimes prevented changing the pingers between nets every 2 days. When this occurred, the 

following period was matched in length of days to the previous observation period (e.g., a 3-day 

3
alarmed period was followed by a 3-day unalarmed period). Pingers were switched between nets 

when the nets were checked to remove fish and any entangled porpoise. The nets were checked 

once each day during mid-morning to late afternoon by the fishing crew unless weather conditions 

compromised the crew’s safety. Any missing or defective pingers were replaced. Each net 

required about 20-30 minutes to be checked. 

An observation team, which was unaware of the status (i.e., alarmed or unalarmed) of the 

nets, conducted 30- to 45minute systematic watches of the field of view. One observer scanned 

the inshore area while another scanned the offshore area, and a third person recorded data. The 

primary focus of the observation effort was net No. 10 which was closest to the observation site. 

The four-person team included a rest position, rotated every 45 minutes. This fourth position was 

also used to track net buoy locations via theodolite bearings. When only 3 observers were 

available, rotations were made every 30 minutes. Rotations allowed a rest from the search effort 

with every other change in position (Appendix B). 

Searching was conducted through 7 x 50 binoculars (Fujinon), which have a 5.44° optical 

field of view with 14 vertical reticle marks which measure the vertical angle from the horizon 

(0.283” per reticle mark). An internal magnetic compass provided 360° horizontal bearings. 

Tripods were used to steady the binoculars and provide a smooth sweep as observers scanned the 

field of view. Observers continuously scanned horizontally across the survey area. One observer 

scanned left to right and the other right to left. Each horizontal scan required 6-8 minutes. To 

minimize redundant observations of the same surfacing, upon completion of a scan the observer 

switched back to the beginning point of the scan (i.e., left or right) instead of scanning back and 

4
forth. The field of view was divided vertically at 7 reticles (i.e., 1,190 m from the site) to define 

the inshore and offshore areas. 

When one or more marine mammals were seen at the surface, the observer announced the 

sighting and provided the vertical angle (estimated to tenths of retitles), horizontal bearing (via 

the internal magnetic compass in each binocular), species, count, and any comments about 

behavior, etc. The recorder transcribed those data and the time of sighting to the closest second 

and the observer’s initials on the data forms (see Appendix B for details). Observers made no 

attempt to avoid re-sighting the same porpoise. Porpoise may have been recorded multiple times 

on different viewing sweeps. Nor was there any attempt to track porpoise though the field of 

view. 

Environmental conditions (i.e., visibility, wind, weather and glare) were recorded at the 

beginning of each watch period and whenever conditions changed during the watch (Appendix B). 

Watch effort was generally suspended when visibility was less than fair or when more than 20% of 

the field of view was obscured by glare. 

Analysis 

Our primary interest was whether harbor porpoise were displaced from the region 

surrounding the net when pingers were attached. For each observation of porpoise, we computed 

the closest distance between the porpoise and net No, 10, which was closest to the observation 

site. Because multiple observations of surfacing harbor porpoise through time will obviously not 

be independent, standard statistical distribution tests (e.g., Kolmogorov-Smirnov) that assume 

independence would be invalid. Instead, we constructed distributions for the distance from each 

5
surfacing to net No. 10, when it was either alarmed or unalarmed. Based on a graphical 

examination of the distributions, we chose a distance of 125 m as the radius for a potential 

displacement region and defined the random variable yi = 1 if harbor porpoise were seen surfacing

once or more within the displacement region during day i and yi = 0 if they were not seen in the

displacement region. If the proportion of days in which yi = 1 (p = Pr [yi, = 1]) were significantly

different between alarmed (pa) and unalarmed (pu) periods, we would conclude that the alarms 

displaced the porpoise. If the amount of observation time and conditions were the same for each 

day and the occurrence of harbor porpoise in the displacement region was independent between 

days, a simple test of equality of binomial proportions could be conducted with Fisher’s exact test 

for a 2 x 2 contingency table (Fleiss 1973). 

Unfortunately, weather conditions varied substantially during our survey, resulting in large 

daily differences in the amount of observation time and visibility conditions. This did not preclude 

performing a valid test because the alarm status of the net was independent of the weather 

conditions except that alarmed or unalarmed periods were sometimes extended when the net 

could not be checked. However, variation in weather conditions could decrease the power of the 

test. If observations between days were assumed to be independent, we could have used logistic 

regression to account for variation in observation effort and test for an alarm effect. However, 

we were not entirely satisfied with the assumption of independence between days, so we used 

hidden-Markov chain models (Satten and Longini, 1996; Zucchini and Guttorp, 1991) to allow 

for possible dependence in the observed sequence y1, yz,. ..,yn. 

A hidden Markov-chain model assumes that the true state of the system is a Markovchain, but the observed state of the system is subject to measurement error. In this case, the true 

6
state of the system is s =l if porpoise surfaced within the displacement region at some point i

during day i but the observed state of the system yi is 1 if the porpoise are seen and 0 if the 

porpoise are not seen. Clearly, if s = 0, then y = 0. If the sequence of s are assumed to be first­ i i i

order Markov, then si

 depends on si-1 but no other states. However, the yi do not satisfy the

Markov property, and y is dependent on y1,y2,...,yi-1 i -, because of measurement error, even if the

errors are independent. Dependence in the errors (e.g., contiguous bad weather days) creates

further dependence in the yi. The probability of seeing harbor porpoise in the displacement region

(yi = 1) given they surfaced within the region (si = 1) was formulated as a logistic equation :

where h is a covariate. We examined the amount of observation time and the average visibility

condition (weighted by search time) during the day as potential covariates.

We considered five different models to describe the state of the system .( si ) (Table 2) to

account for differences in dependence assumptions and a potential alarm effect (xi = 1 if net No. 10

was alarmed on day i and 0 if it was unalarmed) . Models 1 and 2 assume independence between 

days, and Models 3 to 5 allow for dependence between days. Likelihood ratio tests were used to 

test the significance of the covariates and between hierarchical models to test for dependence and 

for an alarm effect. More specific details of the models and the likelihoods and computations are 

given in Appendix C. 

7
RESULTS

Harbor porpoise groups were sighted on 501 occasions in our 135.7 hours of observation 

effort during 27 days (Table 3). Group size varied from 1 to 10 porpoise with 72% either one or 

two porpoise. The amount of observation time varied between 0.3 and 9 hours/day in excellent to 

fair visibility conditions. When the alarm status of net No. 10 changed mid-day, shown as two 

entries for the same date in Table 3, we excluded the afternoon portion of the observation from 

the analysis so we did not have to model dependence within a day as well as between days. This 

excluded 14.3 hours of observation effort, resulting in 50.4 hours of observation effort during the 

13 days when net No. 10 was unalarmed and 7 1 hours during the 14 days when net No. 10 was 

alarmed. 

All of the measurement of buoy positions for net No. 10 were within 40 m of the average 

position. However, it was apparent that on 23 July the inner buoy had shifted and remained 50 m 

to the southeast from its original position. Using separate averages for 11-22 July and 23 July - 6 

August, 96% of the positions were within 20 m of the average, and no measurement exceeded 30 

m from the average. Therefore, distances between harbor porpoise sightings and net No. 10 were 

computed using the average position of net No. 10 during the respective two periods. 

Harbor porpoise sightings were primarily clustered to the north of net No. 10 (Fig. 2) but 

when net No. 10 was unalarmed, harbor porpoise were seen closer to the net. The distribution of 

distances between sightings and net No. 10 (Fig. 3) suggested porpoise were displaced 100 to 

150 m from the net. We chose 125 m as the radius of the displacement region for testing the 

significance of an alarm effect. 

8 
Harbor porpoise were seen within the displacement region on 5 of the 13 days when the 

net was not alarmed, but on only 1 of the 14 days when the net was alarmed (Table 4). Without 

considering the influence of the length of the observation effort and visibility, this is not a 

significant result (P = 0.08, Fisher’s exact test), But, during seven unalarmed and five alarmed 

days when fewer than four observation hours were conducted (Table 4), harbor porpoise were 

never seen within the displacement region. Whereas, during days in which four or more hours 

were observed, harbor porpoise were seen in all but 1 unalarmed day, but on only 1 of 9 alarmed 

days. Fisher’s exact test yields a significant result (P = 0.01) when the analysis is restricted to 

days with four or more hours of observation effort. Visibility does not appear to be an important 

variable, except that there were fewer hours of observation on days when observations were 

halted because of poor visibility conditions. 

Given the clear pattern presented in Table 4, it was not surprising that examining the data 

based on parametric models produced the same conclusions. Each of the five models was fit 

to the observed sequence and included the hours of observation as a covariate in Equation (1) 

(Table 5). In each model, the estimated intercept for Equation (1) was the lower bound of -100, � 

and the slope coefficient for hours was 24.5. Decreasing the lower bound would change the 

highly correlated parameter estimates, but it did not substantially affect the log-likelihood value or 

model predictions. The logistic curve effectively separated the data into two classes as in Table 4: 

1) for days with fewer than 4 hours of observation effort observers had nearly zero probability of 

seeing a harbor porpoise that entered the displacement region sometime during the day, and 2) for 

days with more than 4 hours the observers almost certainly saw porpoise that entered the region. 

We expect that a smoother curve would be observed if the sample size was larger. The number of 

9
observations hours was a very important covariate when tested for model 2 and 4 (Model 2: 

2

x = 13.02, df= 1, P < 0.001, Model 4: x2

 = 15.7, df = 1, P < 0.001). A comparison of Models 

2 and 4 does not give strong evidence for dependence (x2 = 3.92, df = 2, P = 0.14); therefore, 

Model 2 is the most parsimonious model. However, whether we assumed independence between 

days (Model 1 vs. Model 2: x2

 = 6.82, df = 1, P = 0.009) or used the hidden Markov-chain 

model with first-order dependence (Model 3 vs. Model 4: x2

 = 10.7, df = 2, P = 0.005), the 

presence of pingers significantly reduced the probability a harbor porpoise surfaced within 125 m 

of net No. 10. 

DISCUSSION 

Our finding that harbor porpoise were seen less frequently in the vicinity of a net with 

acoustic alarms was the most logical explanation for the reduction in entanglement and 

subsequent mortality in experiments conducted with pingers. We expected harbor porpoise to 

avoid the nets by a considerable distance because the work of Kastelein et al. (1995) 

demonstrated that captive harbor porpoise kept in close proximity of a net became entangled in a 

net even when they were aware of its presence. The captive porpoise eventually learned to avoid 

the net after repeated entanglements, but in a natural setting, learning is not possible because the 

initial entanglement will most likely result in death. While our result refines the possible set of 

explanations, it does not entirely elucidate the mechanism for mortality reduction. 

Whether the porpoise are repelled or alerted by certain pinger frequencies or whether they 

are following their primary prey, herring (Gear-in et al. 1994), that are repelled remains uncertain. 

Differentiating between these mechanisms has important implications on the effectiveness of 

10
pingers and the available management options to reduce entanglement mortality. If harbor 

porpoise are repelled, the potential exists for habituation to the sound and a decline in the 

effectiveness of pingers. However, habituation may not be an important concern for the Makah 

setnet fishery because the fishing season only lasts 2 to 3 months during the summer. If porpoise 

are following herring that are repelled, presumably habituation is less likely. However, reductions 

in herring abundance and availability could reduce the effectiveness of the pingers if the porpoise 

switch to different prey that could be unaffected by the pingers. 

Displacement of porpoise from the area around the net results in mortality reduction, but 

also reduces the available porpoise habitat. We have demonstrated that alarmed nets changed the 

distribution of porpoise within at least 125 m of the net. This area could be potentially larger, and 

we note that the encounter rates of porpoise were also substantially lower when net No. 10 was 

alarmed. We did not analyze these data because it can be easily explained by porpoise moving to 

the north out of the observer’s field of view. While this loss of habitat may not be important for 

the current size of the Makah setnet fishery, historically nets were set throughout the Spike Rock 

Fishery Area and would likely exclude porpoise from the entire area if each net was alarmed. 

ACKNOWLEDGMENTS 

Observers on the shore team included Lisa Baraff, Melissa Dolan, Brad Hanson, Scott 

Hill, Rod Hobbs, Jeff Laake, Sally Mizroch, Marcia Muto, Simona Perry, David Rugh, Kim 

Shelden, and Janice Waite. The acoustic team consisted of Rindy Anderson, Eric Berg, Heidi 

Stinson, and Larry Wolski. Vern Toliver and John Cooke provided logistical support. Pat Gearin, 

Merrill Gosho, Dan Greene, Dan Greene Jr., Rebecca Monette, and Larry Cooke set and attended 

11
the nets as part of the entanglement study and supported the acoustic crew. Anne York reviewed 

the manuscript and discussions with her led to the hidden-Markov chain analysis of the data. We 

appreciate the support of the staff at the Olympic Coast National Marine Sanctuary. Buoys for 

acoustic measurements were attached to the sea floor under OCNMS permit No.04-96. We thank 

the Makah Tribal Council for providing permission to camp on their property next to the Olympic 

National Park. We also thank Makah Forestry who provided access to the Shi Shi trail and the 

Makah National Fish Hatchery for logistical support. This project was supported by funds 

provided to the National Marine Mammal Laboratory, Alaska Fisheries Science Center, by the 

Office of Protected Resources, NMFS, to support the Marine Mammal Protection and 

Endangered Species Acts. Robert DeLong and Douglas DeMaster provided administrative 

oversight. 

12
CITATIONS

Fleiss, J. L. 1973, Statistical methods for rates and proportions. John Wiley & Sons, New York. 

223 p. 

Fullilove, J. 1994 How to make a gillnet “pinger”. N. Fisherman 75(1):29-30. 

Gearin, P. J., M.E. Gosho, L. Cooke, R. L. DeLong, J. L. Laake, and D. Greene. 1996. 

Acoustic alarm experiment in the 1995 northern Washington marine setnet fishery. 

Unpubl. Rep. Available Alaska Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, 7600 Sand 

Point Way NE, Seattle, WA 98115-0070. 

Gearin, P. J., S. R. Melin, R. L. DeLong, H. Kajimura, and M. A. Johnson. 1994. Harbor 

porpoise interactions with a chinook set-net fishery in Washington state. Rep. Int. Whal. 

Commn. Spec. Issue 15:427-438. 

Kastelein, R. A., D. de Haan, C. Staal, S. H. Nieuwstraten, and W. C. Verboom. 1995. 

Entanglement of harbour porpoises (Phocoena phocoena) in fishing nets. Pages 91- 153, 

In: P.E. Nachtigall, J. Lien, W.W.L. Au, and A.J. Read (editors), Harbour porpoises ­

laboratory studies to reduce bycatch, De Spil Publishers, Woerden, The Netherlands. 

13
Kraus, S., A. Read, A. Solow, K. Baldwin, T. Spradlin, E. Anderson, and J. Williamson. 1997. 

Acoustic alarms reduce porpoise mortality. Nature 388:525. 

Reeves, R. R., R. J. Hofinan, G. K. Silber, and D. Wilkinson. 1996. Acoustic deterrence of 

harmful marine mammal-fishery interactions: proceedings of a workshop held in Seattle, 

Washington, 20-22 March 1996. U.S. Dep. Commer. NOAA Tech. Memo NMFS-OPR10, 70 p. 

Satten, G. A. and I. M. Longini. 1996. Markov chains with measurement error: estimating the 

‘true’ course of a marker of the progression of human immunodeficiency virus disease. 

Appl. Statist. 45(3):275-309. 

Zucchini, W., and P. Guttorp. 1991. A hidden Markov model for space-time precipitation 

Water Resour. Res. 27(8): 1917- 1923 

14
Figure 1. -- Spike Rock Fishery area. Approximate field of view (56° indicated by lines 

emanating from base camp position. Net positions (Nos. 10-13) are indicated 

by anchors. Approximate bathymetric contours are indicated for 4,6,8, and 10 

fathoms. 
16
Figure 3. -- Cumulative distributions of distances between harbor porpoise sightings and 

net No. 10 when the net was alarmed and unalarmed. 

17
Table 1. -- Distances between nets (using the center of each net) and the observation site (camp). 

Table 2. -- Potential models, their dependence assumptions, and number of parameters needed to 

describe the state of the system (s). i

18
Table 3. -- Summary of hours watched and number of harbor porpoise observations classified by date, pinger state for net No. 10 

and visibility code (excellent (l), very good(2), good(3), fair(4)). Rows marked with an asterisk were excluded from 

the analysis to reduce dependence. A superscript 1 indicates that one or more observations were made within 125 m 

of net No. 10. An asterisk represents an observation period that was excluded during the latter portion of the day after 

alarm status changed. 
Table 4. -- Proportion of observation days in which harbor porpoise were seen within 125 m of 

net No. 10, classified by alarm state of net No. 10, number of observation hours, and 

visibility conditions. 

Table 5. -- Log-likelihood values and estimated state model parameters (see Appendix C for 

definitions) for models l-5 with hours of observation as a covariate. 

20
Appendix A 

Details of Cliff-height Computation 

21
The height of the cliff was determined from a known beach measurement and alternatively 

from a known distance between the survey site and a landmark, Spike Rock. Points near the 

waterline were marked on the beach at the northernmost (N) and southernmost (S) limits of the 

field of view from the survey cliff-site (C) (Appendix Fig. A-l). The distance between the beach 

points, a, was measured with a tape. A theodolite positioned on a tripod 1.45 m above the cliff 

was used to measure vertical angles and the horizontal angle a. The theodolite was 

then positioned at each of the beach points to measure the horizontal angles (B and y). The sides 

b and c were computed with the following trigonometric relationships for the oblique triangle 

BSN: 

From the vertical angles the height of the cliff, h, can be computed based on the right 

triangles CBN and CBS using: 

From the measurements made (Appendix Table A-l), determinations for h of 44.85 m and 

44.78 m were made based on the vertical angles for the south and north points respectively for an

average of 44.82 m. The beach measurements were made on 9 July 1996 between 1130 and 

1200 h. The high tide at 0848 h was +2.07 m and low tide at 1410 h was +0.58 m. The tide at 

the time of measurement was approximately +1.3 1 m. The beach points were slightly above sea 

level to avoid working in the surf Using the theodolite, the height of the points above sea level 

was measured as the difference in the height of the theodolite above the beach point and a parallel 

23
height above a tidepool at sea level. The average height of the beach points above sea level was 1 

m. Thus, the height of the theodolite above sea level for a 0 m tide was 47.13 m. 

Alternatively, the height, h, can be computed from the known distance, d, to an object 

and the vertical angle <BCK denoted (Appendix Fig. A-2) with the following equation: 

where R = 6,366 km is the Earth’s radius. The second term in the above equation makes a 

correction for the Earth’s curvature. We used this approach by obtaining the distance from an 

imaginary point below the cliff-site position (B) and the base of Spike Rock (K) as d and 

measured the vertical angle, from the cliff-site to the water level at the base of Spike Rock. 

From this computation, the height of the theodolite above sea level at the time of the 

measurement was 44.90 m. The vertical angle measurement was taken at 1127 h on 9 July, so the 

correction of +1.3 1 m for the tide, provides a height of the theodolite above sea level for a 0 m 

tide of 46.21 m. 

The difference in these estimates is easily explained when you consider the difficulty of 

determining the base of Spike Rock at a distance of nearly 2 nautical miles (nmi). We believe the 

beach measurement approach provides an inherently more accurate measurement of the cliff 

height. The observer’s eye level varied somewhat and was about 0.3 m below the theodolite 

because the observers were sitting in chairs. Therefore, for observations a height of 46.83 m was 

used for a 0 m tide. Adjustments to the height from tide variations were made by linear 

interpolation between the daily highs and lows. 

24
Appendix Figure A- 1. -- Geometric representation of cliff-height measurement (h) at point C to 

beach positions N and S. 

Vertices 

C - survey site on the cliff above the beach 

N - north marker on the beach 

S - south marker on the beach 

B - point beneath C, such that the plane containing B, S and N is 

perpendicular to the line CB 

Angles Sides 

a - the horizontal angle, <NBS a - measured length of side NS 

B - the horizontal angle <BSN b - length of side BN 

y - the horizontal angle < SNB c - length of side BS

 - the vertical angle < SBC h - length of side CB, the cliff 

e - the vertical angle <NBC height above sea level 

25
Appendix Figure A-2. -- Geometric representation of cliff-height 

measurement (h) at point C (survey site) to 

position K (Spike Rock) at known distance d. 

26
Appendix Table A-l. -- Geometric measurements and computed values for height determination. 

27
Appendix B

Field Procedure Details

29
PROCEDURES FOR RECORDING HARBOR PORPOISE SIGHTINGS 

FROM A SHORE-BASED OBSERVATION SITE 

Use the OBSERVATION EFFORT form to record systematic search effort. Use the SIGHTING FORM to 

systematically record observations of marine mammals as seen from a shore-based site. Use the TRACKING 

FORM for logging locations of the buoy markers. Use the “Green Book” to record general descriptions of daily 

events, including personnel changes at the observation site, problems encountered, and summary notes. 

OBSERVATION EFFORT 

Location: Enter “Boundary” for the observation site on the bluff northeast of Shi Shi Beach 

(height 46.8 m). If alternate sites are used, give them descriptive names and establish their 

altitudes. 

Date. Enter date as indicated. Only one date per page. 

Page / : Show which page and number of pages in a series. A series consists of all hand-logged data 

from the same day. Pagination should start with “Observation Effort,” then “Sighting Form,” 

then “Tracking Form.” This helps keep track of how many pieces of paper are associated with 

each day’s effort. 

Time: Use militaty hours (1:00 pm = 13:00:00). Each day, synchronize time with the acoustic team. 

Record time to the second. Indicate the time a systematic watch is truly in effect, not the time an 

observer is in place starting to prepare for a watch. 

Observer: Enter initials (see attached listing). 

Position: Record the role the observer is taking, as determined by the field needs (i.e, inshore vs. offshore). 

When the entry is for the end of a watch, write “OFF” in the “Position” column. 

Recorder: Initials of the data recorder. 

[update the following entries each watch rotation or with each significant change of conditions. Sea state and 

visibility conditions are recorded separately for the inshore-offshore observers.] 

Viz: Visibility is a sightability index; it is a record of how well you can see porpoise, not the visibility of the 

horizon. Primary considerations in establishing visibility are 1) an observer’s attentiveness, 2) light level and 

direction, 3) rain or fog, and 4) sea state. 

EX = excellent: Clear skies or high clouds; no problem with light or glare; horizon is

 visible; sea state does not compromise sightability of porpoise. The effective sighting

range is >l mni (<7 retitles).

VG = very good: Clear skies or some cloud cover; very little problem with light level,

glare, or sea state. The effective sighting range is out to nearly 1 mni (7 retitles) with

hardly any interference.

GO = good: Weather may be cloudy, hazy, light fog, or clear; some visibility

interference with low light level, flat light, glare, or sea state (choppy or large swells).

The effective sighting range is out to 0.5 mni (14 retitles) without any interference.

FA = fair: Weather may be cloudy, very hazy, foggy, rainy, or clear; visibility

interference is occurring because of low light level, glare, fog, rain, or sea state

(Beaufort 2 or higher). The sighting range out to 0.5 mni (14 retitles) is somewhat

compromised.

PO = poor: Visibility is badly compromised by near darkness, extreme glare, rain, fog,

choppy seas, or a high surf. Effective sighting range is under 0.3 mni (>21 reticles).

UL = useless: The watch effort is ineffective due to darkness, heavy rain, thick fog, or a

wind storm.

Wind. Beaufort Scale. 

WX: Weather that affects the standard viewing area; indicate only the condition which affects the view 

the most. CL = clear (0-10% overcast); HOV = high overcast, such as cirrus (indicate percent); 

LOV = low overcast, such as cumulus (indicate percent); LF = light fog; HF = heavy fog; LR = 

light rain; HR = heavy rain. 

31 
Glare: Describe glare only as it affects the standard search area. N = none; M = moderate; X = extreme. 

Comments: Note any elements that might affect the search other than those recorded above. 

SIGHTING FORM 

Observers are searching different parts of the study area. We are not conducting a “double-blind” study; therefore, 

we have an open communication about sightings. However, if one observer calls out a sighting, the other observer 

should not change their search routine. 

Each sighting is treated as a new entry. If links between sightings are evident, note them in the 

“Comments” column. If there is a rapid series of surfacings in view, try to record the minutes 

and seconds of each surfacing with locations on as much of the group as is possible. 

Time: Record time to the second when making sightings. 

Vertical: Use the 14 vertical reticle marks in the 7x50 Fujinon binoculars (17’ per reticle mark). 

the marks are of two different widths, treat them as equal, running from 0 at the topmost to 14 at 

the bottom. Subdivide to tenths of an increment as best you can. Count retitles from the sighting 

up to the horizon. If horizon is not clear (i.e., obscured by haze, fog or rain), estimate the 

number of retitles and write “E” next to the reticle reading. 

Bearing: Give the magnetic bearing to the target (as read in the binocular). 

Sp: Enter PP for harbor porpoise; EL for sea otter; ER for gray whale; ZC for California sea lion; EJ for 

Steller sea lion; PV for harbor seal. Also use this column when making entries of other targets, 

such as boats or buoys. 

Count: How many of the target species occurred at the given time and location? 

separated sightings, they should be entered on different data rows and each recorded as a count of 

1, even though the two animals appeared to be traveling together. Use the “Comments” column 

to note your observations of apparent associations. 

Obsv: Record the initials of the observer who called the sighting. 

Comments: Make long comments on the back of the form, and write “Over” in the “Comments” column. 

Comments may include animal’s direction of travel (in magnetic bearing from 0° to 360°) 

behavior (slow, fast, milling, pop-splash, etc.), apparent group size (if a group was too far apart 

in time or space to be combined in the “Count” column), etc. 

TRACKING FORM 

Entries are self-explanatory. Include instrument height and station altitude in the “Alt” entry. Record buoy 

positions at the start of each day and approximately every two hours afterwards. 

[The NT2A theodolite is accurate to 20” with a 19-power lens and an optical field of view of 1.50°.] 

OBSERVERS 

LB = Lisa Baraff MD = Melissa Dolan BH = Brad Hanson SH = Scott Hill 

RH = Rod Hobbs JL = Jeff Laake SM = Sally Mizroch MM = Marcia Muto 

DR = David Rugh KS = Kim Shelden JW = Janice Waite 

ROTATION SCHEDULE 

4 person team - 45 minute periods ­ 2 observers; 1 recorder; 1 rest 

Pattern: Observer -> Rest -> Observer -> Recorder 

3 person team - 30 minute periods - 2 observers; 1 recorder 

Pattern: Observer 3 Recorder -> Observer 

Rotate through this pattern for 3 periods, and then the entire team rests for 30 minutes. After each set of 4 periods, 

observers should have rotated through the starting positions. This does mean each person will have 1 hr search 

periods when 2 observation periods are contiguous. 

32 
TRACKING FORM

OBSERVATION EFFORT

Time Observer Position Recorder Viz Wind WX Glare Comments 

SIGHTING FORM 

Location: Date: Page / 

Time Vertical Bearing Sp Count Comments 

33
Appendix C 

Analysis Details 

35
The state of the system si

 on day i is either 1 if porpoise used the defined region around

the net, or 0, if porpoise did not use the region. For day i, xi

 = 0 if the net was not alarmed and

Xi = 1, if the net was alarmed and hi is the number of hours the net was observed. The observed

state of the system yi at time i is either 1 if porpoise were observed in the defined region around

the net, or 0 if the porpoise did not use the region or used the region but were not seen. The 

relationship between the true and observed system states can be expressed as: 

where p*(hi

) is the probability that porpoise are observed using the region with hi hours of 

observation, modeled as a logistic: 

Each yi is a Bernoulli random variable that has probability p that y = 1 and probability l- i i

pi that yi = 0. The y are assumed to be conditionally independent given the values of pi

. i

Depending on the assumptions, pi may depend on the previous values of y, ,..., yi-1 as influenced

by the true states of the system, s, the alarm states of the net, x , and the hours of observation (hi

) i i

at each previous day: 

The likelihood function conditioned on the first observation is: 
For a model which assumes that the si

 are independent: 

For Model 1, with no alarm effect 

and for Model 2 with an alarm effect: 

where 0 < < 1. The independence models could use all n observations, but the first observation 

was dropped to allow comparisons with the dependence models. 

For a hidden Markov-chain model with first-order dependence 

and for i>3, 

where 

38 
and, 

For Model 3 with first-order dependence of s but no alarm effect:. i

For Model 4, with first-order dependence of s and an alarm effect: i

For Model 5, with first-order dependence of s and alarm effect for current and previous states: i

Allowing for dependence on the previous state requires some assumption regarding the 

beginning of the experiment to compute the likelihood. The options are either to condition on the 

first state or to assume the process has been going for an infinite amount of time and is at 

equilibrium. We chose the former because the pingers had been used for a short time prior to 

initiating observation. Conditioning on the first state requires knowing the true value of the first 

state, s1. If y1 = 0, as it was in this particular case, s1, is unknown. However, we have assumed 

that s1 = y1 = 0 in this case because h1 = 5.7 hours and p*(5.7) = 1 for our data. We fitted 

models that assumed that s1 was 0 and 1, effectively treating s1 as a parameter, and s1 = 0 was 

more likely. 

39 
The calculation of the p1 is recursive. To take advantage of the recursiveness the 

likelihood was re-written as: 

where 

These recursive computations were used to compute the likelihood of the parameters for the 

observed data vector with Splus routines. The parameter values that maximized the likelihood 

were obtained using the Splus routine NLMINB. 

40
RECENT TECHNICAL MEMORANDUMS

Copies of this and other NOAA Technical Memorandums are available from the 

National Technical Information Service, 5285 Port Royal Road, Springfield, VA 22167 

(web site: www.ntis.gov). Paper and microfiche copies vary in price. 

AFSC83 RUTECKI, T. L., M. F. SIGLER, and H. H. ZENGER JR. 1997. Data report: National Marine Fisheries 

Service longline surveys, 1991-96, 64 p. NTIS number pending. 

82 MARTIN, M. H. 1997. Data report: 1996 Gulf of Alaska bottom trawl survey, 235 p. NTIS No. PB98­

103930. 

81 LAUTH, R. R. 1997. The 1996 Pacific West Coast upper continental slope trawl survey of groundfish 

resources off Washington and Oregon: Estimates of distribution, abundance, and length composition, 

156 p. NTIS No. PB97-206912. 

80 LAUTH, R. R. 1997. The 1965 Pacific West Coast upper continental slope trawl survey of groundfish 

resources off southern Oregon and northern California: Estimates of distribution, abundance, and length 

composition, 110 p. NTIS No. PB97-208920. 

79 LAUTH, R. R., M. E. WILKINS, and P. A. RAYMORE JR. 1997. Results of trawl surveys of groundfish 

resources of the West Coast upper continental slope from 1969 to 1993, 342 p. NTIS No. PB97-208904. 

78 HILL, P. S., D. P. DEMASTER, and R. J. SMALL. 1997. Alaska marine mammal stock assessments, 

1996, 150 p. NTIS No. PB97-203277. 

77 CHUMBLEY, K., J. SEASE, M. STRICK, and R. TOWELL. 1997. Field studies of Steller sea lions 

(Eumetopias jubatus) at Marmot Island, Alaska, 1979 through 1994, 99 p. NTIS No. PB97-203376. 

76 OSMEK, S., J. CALAMBOKIDIS, J. LAAKE, P. GEARIN, R. DELONG, J. SCORDINO, S. JEFFRIES, and 

R. BROWN. 1997. Assessment of the status of harbor porpoise (Phocoena phocoena) in Oregon and 

Washington waters, 46 p. NTIS No. PB97-196436. 

75 WING, B. L., C. W. DERRAH, and V. M. O’CONNELL. 1997. Ichthyoplankton in the eastern Gulf of 

Alaska, May 1990, 42 p. NTIS No. PB97-174379. 

74 WILSON, C. D., and M. A. GUTTORMSEN. 1997. Echo integration-trawl survey of Pacific whiting, 

Merluccius productus, off the west coasts of the United States and Canada during July-September 1995, 

70 p. NTIS No. PB97-174367. 

73 CELEWYCZ, A. G., and A. C. WERTHEIMER. 1997. Suitability of Dry Bay, southeastern Alaska, as 

rearing habitat for juvenile salmon, 19 p. NTIS No. PB97-161343. 

72 KINOSHITA, R. K., A. GREIG, D. COLPO, and J.M. TERRY. 1997. Economic status of the groundfish 

fisheries off Alaska, 1995, 91 p. NTIS No. PB97-161269. 

71 STRICK, J. M., L. W. FRITZ, and J. P. LEWIS. 1997. Aerial and ship-based surveys of Steller sea lions 

(Eumetopias jubatus) in Southeast Alaska, the Gulf of Alaska, and Aleutian Islands during June and July, 

55 p. NTIS No. PB97-144026. 

70 EBBERTS, B. D., and B. L. WING. 1997. Diversity and abundance of neustonic zooplankton in the north 

Pacific subarctic frontal zone, 34 p. NTIS No. PB97-136216. 

69 SINCLAIR, E.H. (editor). 1996. Fur seal investigations, 1994, 144 p. NTIS No. PB97-129456.