Response for project 198910700: Statistical Support For Salmon
Comment on proposed FY 2006 budget
The UW confirms its request for renewed funding in 2006 and confirms this budget is consistent with BPA's approved budget.
Accomplishments since the last review
Produce Plan | 2003: Total of 268 hours provided to assist NOAA Fisheries, USACE, USGS, WDFW, Mid-Columbia PUDs, and the Nez Perce Tribe in the design and analysis of salmonid survival studies. | |
Produce Plan | 2003. Skalski. Statistical analysis plan for the 2003 Chelan PUD smolt tagging studies at Rocky Reach and Rock Island dams. Prepared for Chelan County PUD. | |
Produce Plan | 2003: Skalski. Description of the statistical analysis of advanced turbine experiment at Wanapum Dam. Prepared for Department of Energy and Grant County PUD. | |
Produce Plan | 2004: Total of 543 hours provided to NOAA Fisheries, USACE, USGS, WDFW, PUDs, Nez Perce Tribe, Confederated Tribes and Bands of Yakama Nation, and Confederated Tribes of the Umatilla Indian Reservation in design and analysis of tagging studies. | |
Produce Plan | 2004: Skalski. Statistical analysis plan for the 2004 acoustic-tag FPE studies at Rocky Reach and Rock Island dams. Prepared for Chelan County PUD. | |
Produce Plan | 2004: Skalski. McNary turbine survival study in 2004 using PIT-tagged smolts. Prepared for Battelle, Pacific Northwest National Laboratory. | |
Produce Plan | 2005: Assist USACE in the evaluation of minimum-gap turbines, fish-friendly turbine, corner collectors, extended-length submersible screens, other occlusion devices, bypass outfall, spill programs, surface collectors and RSWs, spillway deflectors, etc. | |
Produce Plan | 2005: Skalski., J. R. Overview of fall chinook salmon smolt survival and transport study at Lower Granite Dam. Prepared for US Army Corps of Engineers. | |
Produce Plan | 2005: Skalski, J. R.. A statistical approach to estimating survival with seasonal shutdown of the PIT-tag detection system. Prepared for US Army Corps of Engineers. | |
Produce Plan | 2003: Skalski, J. R. Statistical analysis plan for the 2003 acoustic-tag FPE studies at Rocky Reach and Rock Island dams. Prepared Chelan County PUD, Wenatchee, WA | |
Produce Annual Report | 2003: Submitted Annual Report on 19 November that summarized software development and consulting activities focused on improving the design, analysis, and interpretation of salmonid tagging studies conducted in the Columbia Basin. | |
Produce Annual Report | 2004: Submitted Annual Report on 24 November that summarized software development and consulting activities focused on improving the design, analysis, and interpretation of salmonid tagging studies conducted in the Columbia Basin. | |
Produce Status Report | 2004: Published 4 quarterly newsletters of Salmon Insider to publicize features of the CBR website, http://www.cbr.washingon.edu, i.e., inseason forecasts and monitoring of salmonid migration, interactive graphical displays of status and trends monitorin | |
Produce Status Report | 2005: Published quarterly newsletter, Salmon Insider, to publicize features of the CBR website, http://www.cbr.washingon.edu, i.e., inseason forecasts and monitoring of salmonid migration, interactive graphical displays of status/trends monitoring, etc. | |
Produce/Submit Scientific Findings Report | 2003: Johnson, G. E., J. B. Hedgepeth, J. R. Skalski, and A. E. Giorgi. 2004. A Markov chain analysis of fish movements to determine entrainment zones. Fisheries Research 69(3):349-358. | |
Produce/Submit Scientific Findings Report | 2003: McMichael et al. Chinook salmon in the Priest Rapids Project. Prepared for Grant PUD. Battelle, Pacific Northwest Division, Richland, WA. | |
Produce/Submit Scientific Findings Report | 2004: Peven et al. Guideline and recommended protocols for conducting, analyzing, and reporting juvenile salmonid survival studies in the Columbia River Basin. U.S. Army Corps of Engineers, NOAA Fisheries, USGS, and Mid-Columbia PUDs. | |
Produce/Submit Scientific Findings Report | 2004: Skalski and Lady. Analysis of the 2004 Bonneville Dam DIDSON tracking data. Battelle, Pacific Northwest National Laboratory, North Bonneville, WA. | |
Produce/Submit Scientific Findings Report | 2004: Skalski, J. R., and J. Lady. Analysis of the 2004 The Dalles Dam DIDSON tracking data. Prepared for Battelle, Pacific Northwest National Laboratory, Portland, OR. | |
Produce/Submit Scientific Findings Report | 2005: Buchanan et al. Estimating the effects of smolt transportation from different vantage points and management perspectives. North American Journal of Fisheries Management (submitted). | |
Produce/Submit Scientific Findings Report | 2005: Buchanan and Skalski. A life-cycle release-recapture model for salmonid PIT-tag investigations. Journal of Agricultural, Biological, and Environmental Statistics (in prep). | |
Produce/Submit Scientific Findings Report | 2005: Townsend et al. Correcting bias in survival estimation resulting from tag failure in acoustic and radiotelemetry studies. Journal of Agricultural, Biological, and Environmental Statistics (submitted). | |
Develop RM&E Methods and Designs | 2003: Created user manuals for major software packages, i.e., SURPH 2.1, USER 2.1, PitPro 1.0, SampleSize 1.0. Improved data entry capabilities to Program SURPH 2.1. | |
Develop RM&E Methods and Designs | 2003: Developed new statistical models to jointly analyze smolt downstream and adult upstream PIT-tag detections. | |
Develop RM&E Methods and Designs | 2004: Added diagnostic and graphical tools to Program USER to improve interpretation of fitted models. Expanded Program SampleSize to include replicate releases for the estimation of mean survival. | |
Develop RM&E Methods and Designs | 2004: Initial development of Program ROSTER (River Ocean Survival and Transportation Estimation Routine) to provide joint juvenile-to-adult PIT-tag survival analyses. | |
Develop RM&E Methods and Designs | 2004: Developed preliminary statistical models to analyze upriver adult radiotelemetry studies to estimate adult survival, fallback, and straying rates. | |
Develop RM&E Methods and Designs | 2004: Develop user version of Program ROSTER to provide simultaneous analysis of juvenile and adult PIT-tag detections to estimate inriver and ocean survival, as well as transportation effects. | |
Develop RM&E Methods and Designs | 2004: Expand modeling capabilities and develop interactive software for Program ROSTER for alternative model development to test hypotheses on transportation effects on adult survival. | |
Develop RM&E Methods and Designs | 2005: Continue developing and refining statistical theory and approaches to analyzing complex processes of adult upriver migration, fallbacks, and straying. A flexible unified approach to statistically analyzing the data is anticipated by end of 2005. | |
Develop RM&E Methods and Designs | 2005: Enhance Program USER to include the capability of analyzing abundance data from PIT, balloon, radio, and acoustic-tag survival studies. This expansion will extend the utility of the program to a much wider range of investigators. |
The ongoing mission of Project 1989-107-00, since its inception in 1989, has been the development of statistical tools for analyzing fisheries tagging data in the most precise and appropriate manner possible, and providing statistical guidance on the best ways to design large-scale tagging studies. The need for this mission, which supports the goals of the Columbia River Basin Fish and Wildlife Program (FWP) and FCRPS Biological Opinion (BiOp), is continuing, as the technologies for conducting fish tagging studies improve. In the last decade, fisheries biologists have seen the evolution from freeze-brands and coded wire tags (CWT) to passive integrated transponder (PIT) tags, balloon-tags, radiotelemetry, and now, acoustic-tags. With each advance, the technology holds the promise of more detailed and precise information. However, the methodology for analyzing and interpreting the data concurrently becomes more complex as the tagging techniques become more sophisticated. The goal of the project is to develop the analytical tools in parallel with the technical advances in tagging studies, so that maximum information can be extracted on a timely basis. Associated with this mission is the transfer of these analytical capabilities to the field investigators to assure consistency and the highest levels of design and analysis throughout the fisheries community. Consequently, the project develops state-of-the-art statistical software to estimate smolt inriver survival, ocean survival, adult upriver survival, delayed mortality effects, and SARs from PIT-tag, radiotelemetry, and acoustic-tag studies. To this end, statistical programs SURPH, PitPro, USER, and SampleSize were developed. A new program ROSTER, capable of analyzing PIT-tag, life-cycle information, will be available later this year.
FY 2006 goals and anticipated accomplishments
Produce Plan | Provide statistical support to Columbia River investigators on request on the design of tagging studies, i.e., sample size calculations, guidance on the release-recapture designs, etc. | |
Produce Plan | Provide statistical support on request on analysis of tagging studies, i.e., methods in data analysis, modifying statistical software to accommodate unique analysis requirements, and review of technical reports. | |
Produce Annual Report | Produce annual report summarizing software development and consulting activities focused on improving the design, analysis, and interpretation of salmonid tagging studies conducted in the Columbia Basin | |
Produce Status Report | Produce quarterly newsletter, Salmon Insider. | |
Develop RM&E Methods and Designs | Maintain statistical software programs SURPH 2.2, USER 3.0, PitPro 2.0, ROSTER 1.0, and SampleSize 1.3. Update to work on the newer operating systems, PC and UNIX. Respond to user questions, provide manuals, and provide instruction. | |
Develop RM&E Methods and Designs | Expand Program ROSTER to analyze salmonid life history from PIT-tag data to estimate downriver survival of juveniles, upriver survival of adults, ocean survival and transport-inriver ratios. | |
Develop RM&E Methods and Designs | Enhance Program ROSTER to estimate the delayed mortality, percent of smolts transported, net juvenile survival inriver, accounting for transportation and adjusting T/I ratio for delayed differential effects of upriver adult mortality or straying. | |
Develop RM&E Methods and Designs | Develop interactive software to analyze adult radiotelemetry data, adjusting for fallback and straying to estimate inriver survival. The model will be available to analyze UI radiotelemetry data as it becomes publicly available. | |
Develop RM&E Methods and Designs | Examine use of diffusion models to characterize small-scale movement of smolts in CR estuaries. Develop guidelines in design of tagging studies to monitor estuary mitigation projects, estimate residence times and smolt days in the nearshore habitat. |
Tagging studies within the Columbia Basin are extensive, with tens of millions of CWT, over a million PIT-tags, tens of thousands of radio-tags, and thousands of acoustic-tags used annually to obtain life-history information on salmonid stocks. Yet this FWP project is the only project dedicated to providing statistical support for the design and analysis of these tagging studies. This project helps assure cost-effective study design, valid analysis of the data, and proper interpretation of results to best manage water and salmonid resources. Because evaluation of mitigation projects and system recovery depends on performance measures from tagging studies, reliable study designs and data analyses are crucial to the Fish and Wildlife Program and FCRPS BiOp on Remand. The project mission is to ensure that the salmonid tagging studies in the Columbia Basin have the most up-to-date, accurate and valid statistical analyses. Furthermore, to assure that the tagging studies conducted are cost-effective and capable of delivering the desired information in the most effective and timely manner possible to fisheries managers. The mission in 2006 includes delivering statistical models to analyze PIT-tag, life-history data and adult radiotelemetry data crucial to extracting RM&E performance measures. The new statistical models will be capable of estimating not only juvenile inriver survival, but also ocean survival (i.e., Bonneville to Bonneville), adult upriver survival, fallback rates, transportation-inriver ratios, and delayed mortality (i.e., D), along with associated error variances. These new statistical models will provide the most comprehensive analysis of tagging data to date in preparation for assessing recovery and compliance with Fish and Wildlife Program goals.
Subbasin planning
How is this project consistent with subbasin plans?
Work not related to a subbasin plan. This project is consistent with FWP Strategy 6, hydrosystem passage and operations, by facilitating Strategy 9, research, monitoring, and evaluation. This project is consistent with and implements the Research, Monitoring, and Evaluation efforts from the Final UPA for the FCRPS Biological Opinion Remand, Section IV (pages 88-103). Tasks are listed below. Provides consistent application of statistical methodologies for survival estimation across all salmon life-cycle stages to assure comparable performance measures and assessment of results through time. Maximizes learning and adaptive management opportunities. Improves and maintains the ability to responsibly evaluate the success of implemented Columbia River FWP salmonid mitigation programs and dentify future mitigation options. Improves analytical capabilities to conduct research on survival processes of wild and hatchery chinook salmon and steelhead during smolt outmigration. Improves monitoring and evaluation capabilities and assist in-season river management to optimize operational and fish passage strategies to maximize survival. Extends statistical support to estimate ocean survival and in-river survival of returning adults when adult detection facilities are in place. Provides statistical guidance in implementing a river-wide adult PIT-tag detection capability. Develops statistical methods for survival estimation for all potential users and makes this information available through peer-reviewed publications, statistical software, and technology transfers to organizations such as NOAA Fisheries, the Fish Passage Center, US Fish and Wildlife Service, US Geological Survey (USGS), US Army Corps of Engineers (USACE), Public Utility Districts (PUDs), the Independent Scientific Advisory Board (ISAB), and other members of the Northwest fisheries community. Provides, maintains, and improves statistical software for tag analysis and user support.
How do goals match subbasin plan priorities?
This project accomplishes priority work identified by the FCRPS Biological Opinion Remand (Remand), Section IV (pages 88-103) as critical to reaching the long- and short-term targets listed in the 2005-2007 Implementation Plan for the FCRPS ESA Updated Proposed Action (Section V.A., pages 39-40). Under “RM&E Strategy 1: Status Monitoring” (pg. 88, Remand), “regional monitoring of status information such as adult and juvenile fish abundance, distribution, and survival, or environmental conditions that have been identified as key measures of fish performance, is needed for an effective performance based approach.” The main goal of this project is to develop the analytical tools (such as SURPH) and statistical theory to effectively and accurately perform this task on a system-wide or subbasin level, within tributary or hydrosystem corridor. In that same vein, “RM&E Strategy 2: Action Effectiveness Monitoring and Research” again states that research on the effects of hydrosystem and non-hydrosystem actions require a quantitatively rigorous approach (pg. 92, Remand) with well-designed experiments and adequate replication. Programs such as SampleSize 1.3 developed by this project were designed to assist researchers in this, and must be continually adapted to appropriately fit changing conditions. Finally, RM&E Strategy 3 defines critical uncertainties “related to the assessment methods and data required to evaluate future population performance and needed survival improvements. Projects under this strategy are associated with BiOp actions that address large, systematic research needs and improvements in analytical methods required for more robust and confident assessments of population status and needed survival improvements for each ESU” (pg. 100, Remand). The tools and theory developed by this project specifically address this goal, with the intent of making analyses easier and more defensible for all researchers in the Columbia Basin.
Other comments
Project 1989-107-00 provides the financial support to sustain local expertise on the statistical theory of tag analysis at the University of Washington and make it available to the fisheries community. Ideally, each project and each investigator in the Columbia River Basin would invest in the statistical support needed for the successful completion of their study. However, this is an ideal that is rarely if ever attained. Furthermore, there is only a small pool of highly trained scientists in this specialized area of tag analysis here in the Northwest. Piecemeal and fragmented support from various agencies and organizations would be incapable of maintaining a center of expertise. This funding assures the continuity of support needed to assist organizations on an as-needed basis, as well as provides the necessary support to develop the analytical technologies needed in the foreseeable future.