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Summary

Description

The goals of this project are to further develop a framework for estimation of time-varying natural mortality in Pacific salmon stocks based on widely available CWT recovery data, and to develop a set of R/ADMB programs that will allow broad-scale implementation of these methods for West Coast salmon stocks.

The basic ideas and structural framework for this approach have already been developed, and found promising (Hankin et al. 2005, Hankin and Mohr 1993). However, this approach is not routinely used in assessments, in part due to a lack of robust and flexible tools allowing easy application to new datasets. In addition, further analytic work is required to address details of implementation and to better understand sensitivity to observation error and model mis-specification.

To make this approach broadly useful, we will develop efficient, modern, and portable code (e.g., in R) to extract the required inputs from CWT data files and perform the statistical fitting. Because the likelihood surface is high-dimensional, robust and speedy optimization routines are necessary, e.g. using ADMB (Fournier et al. 2012). We will explore adjustments such as estimating standard errors that account for overdispersion (Lambert et al. 2006), and allowing for incomplete brood years, which would expand the scope of datasets to which the model can be applied.

Fournier, D.A., H.J. Skaug, J. Ancheta, J. Ianelli, A. Magnusson, M.N. Maunder, A. Nielsen, and J. Sibert. 2012. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optimization Methods Software 27:233-249.

Hankin, D.G. and Mohr, M.S. 1993. New methods for analysis of coded-wire tag-recovery data. California Cooperative Fishery Research Unit Agreement No. 14-16-0009-1547, Research Work Order No. 32.

Hankin, D. G., G. S. Morishima, J. H. Clark, B. E. Riddell, R. B. Deriso, C. Schwarz, J. C. Garza, and J. B. Scott. 2005. Report of the expert panel on the future of the coded wire tag recovery program for Pacific salmon. Report prepared for the Pacific Salmon Commission. http://swfsc.noaa.gov/publications/fed/00791.pdf

Lambert, D. M., J. M. Hoenig, and R. N. Lipicius. 2006. Tag return estimation of annual and semiannual survival rates of adult female blue crabs. Transactions of the American Fisheries Society, 135:1592-1603.

Mohr, M. S., D. G. Hankin, and T. Speed. unpublished. Estimation of ocean natural mortality rates for Klamath River Fall Chinook salmon based on coded-wire tag recovery data. Unpublished report.

Contact Information

Point of Contact
Shanae D Allen
Shanae.Allen@noaa.gov
(831) 420-3970

Item Identification

Title: Estimation of time-varying natural mortality rates for salmon from coded-wire-tag data
Status: Completed
Abstract:

The goals of this project are to further develop a framework for estimation of time-varying natural mortality in Pacific salmon stocks based on widely available CWT recovery data, and to develop a set of R/ADMB programs that will allow broad-scale implementation of these methods for West Coast salmon stocks.

The basic ideas and structural framework for this approach have already been developed, and found promising (Hankin et al. 2005, Hankin and Mohr 1993). However, this approach is not routinely used in assessments, in part due to a lack of robust and flexible tools allowing easy application to new datasets. In addition, further analytic work is required to address details of implementation and to better understand sensitivity to observation error and model mis-specification.

To make this approach broadly useful, we will develop efficient, modern, and portable code (e.g., in R) to extract the required inputs from CWT data files and perform the statistical fitting. Because the likelihood surface is high-dimensional, robust and speedy optimization routines are necessary, e.g. using ADMB (Fournier et al. 2012). We will explore adjustments such as estimating standard errors that account for overdispersion (Lambert et al. 2006), and allowing for incomplete brood years, which would expand the scope of datasets to which the model can be applied.

Fournier, D.A., H.J. Skaug, J. Ancheta, J. Ianelli, A. Magnusson, M.N. Maunder, A. Nielsen, and J. Sibert. 2012. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optimization Methods Software 27:233-249.

Hankin, D.G. and Mohr, M.S. 1993. New methods for analysis of coded-wire tag-recovery data. California Cooperative Fishery Research Unit Agreement No. 14-16-0009-1547, Research Work Order No. 32.

Hankin, D. G., G. S. Morishima, J. H. Clark, B. E. Riddell, R. B. Deriso, C. Schwarz, J. C. Garza, and J. B. Scott. 2005. Report of the expert panel on the future of the coded wire tag recovery program for Pacific salmon. Report prepared for the Pacific Salmon Commission. http://swfsc.noaa.gov/publications/fed/00791.pdf

Lambert, D. M., J. M. Hoenig, and R. N. Lipicius. 2006. Tag return estimation of annual and semiannual survival rates of adult female blue crabs. Transactions of the American Fisheries Society, 135:1592-1603.

Mohr, M. S., D. G. Hankin, and T. Speed. unpublished. Estimation of ocean natural mortality rates for Klamath River Fall Chinook salmon based on coded-wire tag recovery data. Unpublished report.

Purpose:

Estimates of natural morality are an integral component of stock assessment, and it is known that many results from stock assessments can be heavily influenced by the choice of natural mortality (e.g., biological reference points, Goodyear 1993). Yet, owing to the difficulty of directly estimating natural mortality, fixed external estimates or assumed values are frequently used. Temporal and/or age-dependent variation in natural mortality undoubtedly exists and the assumption of fixed natural mortality likely results in assessment errors. However, estimation of temporal variation in natural mortality in stock assessment has been infrequently performed (Brodziak et al. 2009).

Cohort reconstructions (Hilborn and Walters 1992) performed on tagged cohorts of salmon are the backbone of salmon assessment. Reconstruction of cohorts from coded-wire-tag (CWT) data allows estimation of age-specific abundance, harvest rates, maturation rates, and other vital rates used for salmon management. Assumption of a constant natural mortality rate for adult salmon is required for statistical identifiability when using current techniques that treat cohorts independently (Hankin et al. 2005). Unfortunately, this means that vital rate estimates are biased to an unknown extent by assumed and arbitrary values assigned to adult natural mortality rates. For example, a real increase in the natural mortality rate between age-3 and age-4 in a particular year would be erroneously interpreted instead as unusually high maturation at age-3.

Brodziak, J., J. Ianelli, K. Lorenzen, and R.D. Methot Jr. (eds.). 2009. Estimating natural mortality in stock assessment applications. NOAA Tech. Memo. NOAA-TM-NMFS-F/SPO-119.

Goodyear, C.P. 1993. Spawning stock biomass per recruit in fisheries management: foundation and current use. In Risk evaluation and biological reference points for fisheries management. Edited by S.J. Smith, J.J. Hunt, and D. Rivard. Canadian Special Publications in Fisheries and Aquatic Sciences 120:67¿81.

Hankin, D. G., G. S. Morishima, J. H. Clark, B. E. Riddell, R. B. Deriso, C. Schwarz, J. C. Garza, and J. B. Scott. 2005. Report of the expert panel on the future of the coded wire tag recovery program for Pacific salmon. Report prepared for the Pacific Salmon Commission. http://swfsc.noaa.gov/publications/fed/00791.pdf

Hilborn, R. and Walters, C.J. 1992. Quantitative Fisheries Stock Assessment. Kluwer, London.

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
None age- and time-dependent models
None cohort reconstruction
None fisheries management
None natural mortality
None virtual population analysis

Physical Location

Organization: Southwest Fisheries Science Center
City: Santa Cruz
State/Province: CA
Country: USA

Support Roles

Point of Contact

CC ID: 195287
Date Effective From: 2015
Date Effective To:
Contact (Person): Allen, Shanae D
Address: 110 Shaffer Rd.
Santa Cruz, CA 95060
USA
Email Address: Shanae.Allen@noaa.gov
Phone: (831) 420-3970
Fax: (831) 420-3980
Business Hours: M-F 10:00 - 18:00

URLs

URL 1

CC ID: 195288
URL: https://swfsc.noaa.gov/SalmonAssessment/
URL Type:
Online Resource
Description:

Salmon Assessment Team website

Catalog Details

Catalog Item ID: 24231
GUID: gov.noaa.nmfs.inport:24231
Metadata Record Created By: Shanae D Allen
Metadata Record Created: 2015-03-30 13:33+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2022-08-09 17:11+0000
Metadata Record Published: 2015-12-22
Owner Org: SWFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2015-12-22
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2016-12-22