Ecological Archives A018-045-A1

Richard B. Deriso, Mark N. Maunder, and Walter H. Pearson. 2008. Incorporating covariates into fisheries stock assessment models with application to Pacific herring. Ecological Applications 18:1270–1286.

Appendix A. Tables showing (Table A1) data used in the PWS herring hypothesis testing with the herring population model, (Table A2) estimates and the standard errors of recruitment and adult survival from mortality sources other than fishing are given for the best single-factor model, and (Table A3) estimated parameter coefficients, their standard errors, and corresponding coefficient of variation are given for each of the 19 hypotheses for the model with the additional 1993 mortality parameter.

TABLE A1. Data used in the PWS herring hypothesis testing with the herring population model. Deviates (Dev’s) were calculated by centering the data around its mean and then dividing the difference by the mean. Missing VHSV and I. hoferi values were replaced by averages. I. hoferi values for 2003–2005 were extrapolated from field data. Missing coho return values for 1980–1981 were set to the 1982 value. Pink salmon return values were three-year averages lagged back by one year (such as 1980 value is 1977–1979 average). Coho Salmon values were two-year averages lagged back by one year. Pink salmon hatchery fry releases were two-year averages lagged back by two years (such as 1980 value is 1977–1978 average). Some data were used for multiple hypotheses so the data index count does not match the hypothesis index count. See text for further explanation.

Data Index

1

2

3

4

5

6

7

               

Year

   

Weight at standard length dev’s

Winter GOA temp. dev’s

VHSV all ages

VHSV age 3–4

I. hoferi all ages

I. hoferi ages 5+

Oil exposure TPAH index

               

1980

0.07

0.01

       

1.7

1981

0.02

-0.08

       

1.7

1982

0.04

-0.1

       

1.7

1983

0.10

-0.01

       

1.7

1984

0.01

0.03

       

1.7

1985

0.00

0.13

       

1.7

1986

0.15

-0.01

       

1.7

1987

0.07

0.11

       

1.7

1988

0.04

0.04

       

1.7

1989

0.00

-0.05

       

339.5

1990

-0.06

-0.02

       

5.6

1991

0.00

-0.18

       

2.9

1992

-0.09

-0.02

       

3.7

1993

-0.12

-0.06

       

6.4

1994

-0.10

0.42

14.18

103.88

23.11

23.56

2.6

1995

-0.06

-0.09

8.26

14.24

21.82

26.35

1.6

1996

-0.02

-0.03

0

0

20.46

26.24

1.8

1997

-0.03

-0.09

7.31

9.4

16.15

25.98

1.8

1998

-0.06

0

43.52

59.51

17.6

35.44

2

1999

-0.03

-0.1

0.67

1.05

24.33

30.24

1.2

2000

0.00

-0.13

0

0

21.67

23.85

0.9

2001

0.00

-0.01

1.11

0.64

38

48.57

0.6

2002

0.06

-0.15

9.33

14.35

15

32.89

0.3

2003

0.03

0.18

   

20.4

28.12

0.8

2004

-0.02

0.22

   

28

38.6

1.1

2005

-0.02

     

50.6

69.75

0.1


TABLE A1. Continued.

Data Index

8

9

10

11

12

           

Year

Spawn on kelp pound fishery lbs (107)

Pink salmon hatchery fry (107)

Pink salmon hatchery returns (107)

Coho return (107)

Sea lion abundance non-pup

           

1980

0.24

21.28

1.07

 

6182

1981

0.64

24.9

2

 

6217

1982

0.69

57.64

4.15

0.012

6114

1983

0.63

91.51

4.75

0.01

5892

1984

1

103.53

5.49

0.011

5579

1985

1.81

115.72

6.4

0.01

5200

1986

1.53

153.82

11.06

0.011

4784

1987

3.08

211.42

12.1

0.014

4353

1988

0

225.18

16.45

0.016

3927

1989

2.47

375.44

21.92

0.018

4581

1990

5.06

519.87

29.62

0.022

4001

1991

6.06

561.41

25.95

0.026

3316

1992

2.66

609.33

16.76

0.023

2181

1993

0

549.61

17.56

0.023

2012

1994

0

531.51

19.7

0.024

1842

1995

0

527.95

25.96

0.026

1816

1996

0.58

550.87

22.61

0.039

1402

1997

0.21

632.42

26.71

0.054

1536

1998

0.1

568.1

32.36

0.055

1353

1999

0

513.44

34.96

0.049

1197

2000

0

572.24

35.69

0.12

1399

2001

0

594.37

28.17

0.453

1396

2002

0

603.83

26.77

0.615

1393

2003

0

621.06

23.51

0.411

1408

2004

0

612.24

33.69

0.363

1619

2005

0

605.68

30.89

0.387

1669


TABLE A1. Continued.

Data

13

14

15

16

17

           

Year

Total pink salmon return (107)

PDO fall–winter average

PDO spring–summer average

Northern Oscillation index fall–winter

Northern Oscillation index spring–summer

       

Average

Average

1980

9.28

0.78

0.55

-3.49

-0.3

1981

12.66

0.4

1.06

-1.22

0.76

1982

18.8

0.7

0.04

-1.47

-1.39

1983

20.48

1.36

2.05

-7.38

-1.04

1984

20.62

0.82

0.58

-0.02

0.84

1985

21.94

0.81

0.45

1.58

0.29

1986

23.8

1.71

0.9

-1.86

0.52

1987

22.61

1.28

2

-1.55

-1.66

1988

24.4

-0.56

0.56

1.16

-0.32

1989

19.43

-0.4

0.25

2.85

0.48

1990

23.16

-1.43

0.32

1.17

-0.91

1991

27.96

0.34

-0.35

0.68

0

1992

36.85

0.57

1.29

-3.97

-1.49

1993

32.17

1.05

2.05

-3.19

-2.02

1994

19.34

-0.73

0.11

-0.57

-0.51

1995

19.15

0.45

1.11

-3.63

-0.95

1996

22.01

0.15

0.94

-0.53

0.48

1997

28.79

1.3

2.16

1.24

-2.79

1998

25.29

-0.61

0.15

-5.84

-0.21

1999

30.14

-1.41

-0.92

3.22

0.46

2000

38.11

0

-0.54

0.7

-0.24

2001

42.32

-0.73

-0.76

1.97

0.45

2002

44.24

1.56

-0.1

0.73

-0.73

2003

34.04

0.53

0.77

-1.83

-1.13

2004

39.53

0.28

0.59

0.38

0.17

2005

35.72

0

0.75

-0.88

0.21

 

TABLE A2. Estimates and the standard errors of recruitment and adult survival from mortality sources other than fishing are given for the best single-factor model. The estimate of the coefficient for the effect of pink salmon on recruitment is -0.0028 (0.0010), but this has to be interpreted with respect to the values of the index provided in Table A1. Semester 1 starts the first of May and continues though October and semester 2 starts the first of November and continues through April of the following year.

     

Survival

     

Semester 1

Semester 2

 

Recruitment at age 3

 

Ages 3–8

Ages 9+

Ages 3–8

Ages 9+

Year

Value

SE

Value

SE

Value

SE

Value

SE

Value

SE

1980

416

93

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1981

242

58

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1982

274

65

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1983

790

177

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1984

577

128

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1985

155

40

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1986

156

42

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1987

2495

571

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1988

236

61

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1989

53

26

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1990

62

27

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1991

1394

349

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1992

73

30

0.63

0.05

0.59

0.05

0.63

0.05

0.59

0.05

1993

118

30

0.63

0.05

0.59

0.05

0.81

0.01

0.76

0.03

1994

21

8

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1995

113

26

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1996

64

15

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1997

138

32

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1998

108

27

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

1999

14

6

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

2000

61

16

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

2001

17

7

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

2002

494

133

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

2003

95

30

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

2004

64

23

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

2005

134

47

0.81

0.01

0.76

0.03

0.81

0.01

0.76

0.03

 

TABLE A3. Estimated parameter coefficients, their standard errors, and corresponding coefficient of variation are given for each of the 19 hypotheses for the model with the additional 1993 mortality parameter. Note that in some cases, the coefficient has the opposite sign from that expected by the hypothesis and therefore such results are not valid.

Hypothesis

Coefficient

SE

CV

1

7.71E-01

1.17E+00

151.39%

2

1.25E+00

1.02E+00

82.02%

3

-1.47E-01

1.26E-01

85.54%

4

7.83E-02

9.31E-02

118.98%

5

6.16E-02

1.14E-01

184.54%

6

3.84E-02

3.20E-02

83.43%

7

-4.36E-03

1.10E-02

252.33%

8

2.98E-03

1.82E-03

61.02%

9

1.85E-02

1.33E-03

7.20%

10

5.73E-03

3.98E-03

69.46%

11

-3.17E-02

4.12E-02

130.10%

12

-2.18E-01

3.81E-01

175.23%

13

-9.51E-03

1.52E-02

159.61%

14

-4.56E-02

3.87E-02

84.79%

15

-2.79E-03

9.86E-04

35.38%

16

-3.36E-03

1.45E-03

43.19%

17

-3.84E-02

2.78E-02

72.39%

18

-2.22E-03

1.65E-03

74.30%

19

-3.64E-06

1.27E-05

348.95%


[Back to A018-045]