This project provides quantitative support to the fisheries community from study design through data analysis and interpretation.  Starting from first principles, statistical methods are tailored specifically for the intent of the tagging study objectives.  From the onset, investigators therefore know exactly what information can and cannot be extracted and what model assumptions must be met for a valid study.  By tailoring the statistical models to the specific purpose of the study, maximum precision is also obtained.

The project also develops interactive statistical software to allow investigators to easily and competently analyze tagging data.  Program SURPH was developed to analyze juvenile PIT-tag data; Program USER, to analyze radio- and acoustic-tag studies; Program ROSTER, to analyze joint juvenile and adult PIT-tag detections; Program PitPro, to easily and correctly extract detection histories from the PTAGIS data base for the analysis of adult and juvenile survival and transportation studies; Program ATLAS, to analyze acoustic-tag survival studies requiring tag-life corrections; and in development, Program TribPit, to analyze the complex PIT-tag data collected during juvenile outmigration in the headwaters.  Program TribPit SampleSize was developed to help investigators determine tag-release sizes for juvenile studies in the tributaries.  The newest Program BRANCH was developed to analyze the complex movements of smolts and adults in tributaries or estuarine environments.  Technical support is provided to investigators through instruction, consultation, and assistance in the design and analysis of complex datasets.  Program SampleSize was developed to assist investigators in the design of single-release, paired-release, transport-inriver, and balloon-tag survival studies.  Each year, this project assists investigators in the design and analysis of over 20 major tagging studies conducted by state and federal agencies, public utility districts, and tribal organizations in the Columbia Basin.

Tagging studies within the Columbia Basin have become extensive, with tens of millions of CWT, over a million PIT tags, and tens of thousands of acoustic tags used annually to obtain life-history information on salmonid stocks.  Yet, this BPA-funded project is the only project dedicated to providing statistical support for their design and analysis.  This project helps assure cost-effective tagging studies, 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 rely on performance measures from tagging studies, reliable study designs and data analysis are crucial to the Fish and Wildlife Program (FWP).


PROJECT GOAL

Ensure that salmonid tagging studies in the Columbia Basin are conducted with the best available design and analysis, including sample size guidance, state-of-the-art statistical software, and consultation in order to provide cost-effective and precise research, monitoring, and evaluation studies.


PROJECT OBJECTIVES

1. Provide 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, to maximize learning and adaptive management opportunities, and to improve and maintain the ability to responsibly evaluate the success of implemented Columbia River FWP salmonid mitigation programs and identify future mitigation options.

2. Improve analytical capabilities to conduct research on survival processes of wild and hatchery Chinook salmon and steelhead during smolt outmigration, to improve monitoring and evaluation capabilities and assist in-season river management to optimize operational and fish passage strategies to maximize survival.

3. Provide statistically valid estimates of downriver juvenile survival, ocean survival, upriver adult survival, smolt-to-adult ratios, transport-inriver ratios, delayed mortality (i.e., D), transport fractions, age-at-return compositions, and associated standard errors.  Other parameters include adult fallback rates at hydro projects and adult straying rates that are important in understanding the effects of the hydro system on salmonid recovery.

4. Develop statistical methods for survival estimation and make this information available through peer-reviewed publications, statistical software, and technology transfers to the Pacific Northwest fisheries community and the public.

5. Provide and maintain statistical software programs for tag analysis and provide user support.

6. Provide improvements in statistical theory and software as requested by user groups.

These improvements include extending software capabilities to address new research issues, adapting tagging techniques to new study designs, and extending the analysis capabilities to new technologies such as radio tags, acoustic tags, flat-plate PIT-tag detectors in the tributaries, and PIT-tag detections at spillway weirs at hydroprojects.


PROJECT ACCOMPLISHMENTS

Integration, Coordination, and Information Transfer

This project is integrated and coordinated with Columbia River fisheries agencies and Tribes, the Northwest Power and Conservation Council (NPCC), and other scientific expert panels investigating survival processes.  The transfer and coordination of information and products produced by this project has occurred throughout the history of the project.  Information transfer is accomplished by printed technical reports, scientific publications, public presentations, internet-based statistical software products, software training sessions, and one-on-one statistical consulting.  

Biological/Ecological Results to Date

The project spearheaded the PIT-tag survival studies currently being conducted on the Snake/Columbia Rivers (1993-2016).  Monte Carlo investigations identified sensitivities of PIT-tag studies to violations of some assumptions and robustness to other assumptions paving the way for field trials.  In conjunction with NMFS, this study has helped to generate new biological understandings of the dynamics of smolt outmigration.  These findings include:

     1. Information on smolt travel time and survival relationships.
     2. Survival rates for subyearling and yearling Chinook salmon and steelhead smolts throughout the Columbia
         Basin.
     3. Information on river flow/temperature – survival relationships.
     4. Comparisons of hatchery and wild Chinook salmon and steelhead smolt survival.
     5. Comparison of smolt survival across 20 years and 5–8 river reaches.
     6. Baseline survival data for comparison with potential mitigation practices in years to come.
     7. Information on fish guidance efficiency (FGE) and spill effectiveness (SE) relationships at Snake and
         Columbia River dams.
     8. Season-wide estimates of smolt survival.
     9. Route-specific survival and passage probabilities at hydroelectric projects.
   10. Comparison of turbine passage survival and turbine operating efficiency.
   11. Information on transportation effects (i.e. transport/inriver ratios), and adult returns (SARs), and delayed
         mortality (D).
   12. Detection rates of juvenile and adult PIT-tag facilities.
   13. Adult fall-back rates.
   14. Estimates of Bonneville-to-Bonneville survival.
   15. Estimates of Lower Granite to Lower Granite survival of salmonid stocks.
   16. Comparison of survival and migration success of transported and nontransported fish.    
   17. Unidentifiable losses among inriver adult migrant fish.  
   18. Use of hatchery summer Chinook as surrogates for wild Chinook salmon smolt with regard to juvenile survival,
     ocean survival, and upriver adult survival.
   19.  Estimation of adult salmon overshoot rates and fallback rates by project and fish stock.
  
These data have influenced the choices of current mitigation practices and strategies for the future.

In 1998, PIT-tag survival studies were extended to the Mid-Columbia where technical developments from this project were used to design and analyze studies conducted by NMFS and PUDs.  In 1999-2016, smolt survival methods were extended to the use of paired release-recapture studies using PIT-tagged, radio-tagged, and acoustic-tagged releases to estimate survivals at five Mid-Columbia projects.  This BPA program was the inspiration for those investigations based on the 1998 BPA technical report by Skalski et al. (1998).  The findings from these studies include:

   1. Information on river flow/temperature - survival relationships within season.
   2. Comparison of survival rates of hatchery and run-of-the-river juvenile steelhead and yearling Chinook salmon.
   3. Partitioning of project survival into dam and pool components.
   4. Comparison of the outmigration dynamics of PIT-tagged, radio-tagged, and acoustic-tagged steelhead and
       Chinook salmon.
   5. Estimates of route-specific survival through spillways, sluiceways, surface collectors, and powerhouses.
   6. Assessment of smolt survival with Habitat Conservation Plan (HCP) standards.
   7. Technical information on how to best implement single-release, paired-release, and multi-release study designs
        to estimate smolt survival using radio-tag and acoustic-tag studies.

In 2001, this project started to provide statistical support to the smolt survival studies conducted by US Geological Survey (USGS) for USACE at Lower Columbia River dams.  This project provided the statistical models and software to estimate dam passage and route-specific survival estimates.  In 2004, this project worked with USGS to implement a triple-release design at The Dalles Dam to improve estimates of dam passage survival.  This project also assisted USGS in sample size calculations and study design for the 2004 summer spill study at Bonneville Dam.  The findings include:
   1. Estimates of route-specific survival through spillways, sluiceways, and powerhouses.
   2. Comparison of spill and powerhouse passage survival under different operating conditions.
   3. Information on lower river flow/temperature-survival relationships within season.
   4. Baseline survival data for comparison with potential mitigation practices in the future.

Efforts in 2005 on behalf of NMFS, USACE, the Mid-Columbia PUDs, and First Nations fisheries included new applications of radio tags and acoustic tags for the purpose of estimating juvenile passage survival.  The project also assisted NMFS, USACE, and the Mid-Columbia PUDs with the evaluation of its adult PIT-tag detection facilities at adult ladders throughout the Columbia Basin.  

In 2006, this project began a comprehensive effort of estimating ocean and upriver survival of returning adult salmonids using the software program ROSTER.  Program ROSTER software analyzes juvenile and adult PIT-data and also extracts estimates of smolt-to-adult ratios (SARs), transport/inriver ratios (TIRs), and tests for continued effects of smolt transportation on adult upriver migration success.  In 2007, an updated version of Program ROSTER 2.0 was publicly released and a report detailing the tagging results was submitted for public review.

In 2008, this project extended the ROSTER analysis to wild Chinook salmon and steelhead stocks in the Columbia River.  Other significant developments included designing acoustic-tag study plans to differentiate and estimate migration, residualization, and survival rates of subyearling Chinook salmon smolts.  These methods were field tested by USACE in the Lower Granite and Lower Monumental reaches of the Snake River.  In addition, acoustic-tag study designs were developed to estimate the rate of use and benefit of habitat mitigation projects in the Lower Columbia estuary.  

In 2009, an intensive review of field methods to estimate adult escapement (i.e. spawner abundance) found many of the spawner count, carcass count, and mark-recapture techniques produce biased estimates, and that changes in data collection and analyses are warranted.

In 2010, a peer-reviewed publication suggested hatchery summer Chinook salmon smolt may be used as surrogates for wild Chinook salmon smolts regarding migratory success as measured by juvenile survival, ocean survival, adult survival, and SARs.

In 2011, analyses performed using Program ROSTER found ocean survival between 1999 and 2006 to vary tenfold between years (i.e., range of 0.002 [SE = 0.001] to 0.024 [SE = 0.0026]) and constitute an average of 86.2% of the total mortality during Lower-Granite-to-Lower-Granite migration.  Conversely, inriver juvenile survival (i.e., Lower Granite to Bonneville) represented only 9.4% of the total mortality during migration.  .

Over the years 2010-2014, this project designed the compliance tests of smolt passage survival through federal dams as required by the 2008 FCRPS BiOp.  With matching funds from the US Army Corps of Engineers, this project developed the release-recapture model, the statistical software (Program ATLAS), the reporting format, and associated tests of study assumptions.  During this five-year period, this project has assisted in the design and analyses of 29 compliance tests in the FCRPS.  PI is senior author on the reports of the compliance tests in the FCRPS.  

During 2013-2015, this project developed Program BRANCH, which allows investigators to develop statistical models for complex smolt and adult survival and movement studies based on a user-driven graphic interface.  

In 2015, this project developed Program TribPit SampleSize to help investigators determine necessary tag-release sizes for juvenile PIT-tag studies in the tributaries and headwaters of the Columbia Basin.  Program TribPit was also developed to estimate the complex survival processes of steelhead smolts in the tributaries.  This project also worked with regional biologists to verify methods for estimating adult steelhead overshoot and fallback rates.  

In 2016, an extensive effort was implemented to estimate the straying, overshoot, and fallback rates of adult salmonids in the hydrosystem using Program BRANCH.  In addition, this project examined the effect of alternative hydrosystem operations and new PIT-tag detection capabilities on the precision of system-wide estimates of smolt survival.

In 2017, Program Basin TribPIT was released for cohort analysis of juvenile salmonid movement and survival in tributaries within basins.  This software uses multiple juvenile PIT-tag releases within a river basin to estimate cohort survival.  By using multiple release within the same basin, sample size is increased, thereby improving precision of cohort survival estimates.

Nonbiological Results to Date

This project has infused statistical defensibility and reliability into fish tagging studies in the Columbia Basin.  This project did the prerequisite statistical research to launch the first PIT-tag juvenile tagging studies in the Basin in collaboration with NMFS.  The statistical models and software for juvenile PIT-tag survival studies have made those investigations the "gold standard" of survival studies.  Subsequently, the project has developed the statistical models and software to conduct balloon-tag, radio-tag, and acoustic-tag smolt survival investigations used throughout the Basin.  More recently, models to analyze the complex adult PIT-tag (i.e., Program ROSTER), radio-tag, and acoustic-tag data (i.e., Program ATLAS) have been developed.  Currently, the project is working with federal and tribal investigators to develop statistical methods (i.e., Program TribPit) to analyze juvenile flat-plate PIT-tag detections in the headwaters.  Throughout this entire process, project personnel have worked with investigators to transfer this technology to the field staff responsible for collecting much of the monitoring and evaluation data collected in the Basin.

These ongoing efforts have produced statistical software programs for the analysis of salmonid survival studies (e.g., SURPH, USER, TribPit, ROSTER, ATLAS, BRANCH, TribPit SampleSize) that are accessible to the Columbia Basin fisheries community via internet http://www.cbr.washington.edu/analysis.html).  Additional products include user's manuals, software for sample size calculations (i.e., SampleSize 2.0), and software to convert PTAGIS data to databases ready for statistical survival and transportation effects estimation (i.e., PitPro).  In 2005, Program ROSTER 1.0 was made publicly available to analyze joint juvenile and adult PIT-tag data to estimate transport-inriver ratios, SARs,  and delayed mortality (D).  In 2007, an updated version of Program ROSTER 2.0 was released as well as an updated version of PitPro (4.0) that accounts for largely unpublished anomalies associated with the transport program (e.g., transport bypass events).  In 2008, a substantially improved version of Program USER, 4.1, was released that provides a more user-friendly interface and has greater analytical capabilities.  This enhancement effort continued throughout 2009 and culminated in the current Program USER 4.4, with an improved user-friendly interface and greater analytical capabilities.  The new generation of Program SURPH, developed and tested in 2008, was released in 2009 to accommodate new operating systems and provide greater ease of use by both novice and experienced investigators.  The software for Program SampleSize was expanded to include a new model, Virtual with Paired Release, and the interface was redesigned to incorporate a wizard-based user's guidance system.  Released in 2010, Program ATLAS 1.0 is used to model tag-life and provide tag-life adjusted estimates of survival for radio- and acoustic-tag studies.  This program is the basis of all the survival compliance testing performed in the FCRPS under the 2008 BiOp.  In 2011, Program ATLAS 2.0 was upgraded to include estimation of cumulative downriver survival, allow multiple tag-life corrections for different tag lots, and process multiple data runs.  In 2013, Program TribPit was released to analyze juvenile migration and survival in the tributaries and headwaters using flat-plate PIT-tag detections.  In 2013, prototype software was developed that uses a graphical user interface (GUI) to program complex multistate (i.e., branching) release-recapture models for smolt and adult migration analyses based on a user-drawn schematic.  A publicly available version of Program BRANCH was developed in 2014-2015  for release.  In 2016, Program TribPit was greatly expanded to allow juvenile PIT-tag data within entire river basins to be analyzed simultaneously to improve the precision of juvenile tagging studies.

Specific accomplishments by year follow:

1989:  Developed theory to assess survival effects that result from ambient river conditions.

1990:  Began software development for statistical analyses, and began statistical theory to assess individual covariate effects on survival.

1991:  Demonstrated ability to simultaneously assess ambient effects and individual covariate effects.  

1992:  Extended computer software to include analysis of group and individual covariate effects.  Proposed "strawman" design for development of PIT-tag facilities on Snake/Columbia River.  Developed study plan for a Snake River survival study evaluation.

1993:  Completed statistical software development of analysis package--final debugging of computer program, helped facilitate Snake River survival study, and conducted analysis of hatchery survival studies.

1994:  Completed SURPH statistical software and dissemination of a user's manual for statistical analysis of data.

1995:  Produced a PC version of SURPH software and sample size program to design tag-release studies.

1996:  Developed statistical methods for estimating season-wide survival.  Investigated nonparametric methods for improved confidence intervals.  Developed statistical models to estimate fall Chinook salmon smolt survival and residualization probabilities.

1997:  Developed shareware on the internet to convert PTAGIS databases to formats suitable for survival estimation.  Also developed batch routines to conduct large, repetitive data analyses of survival studies.

1998:  Demonstrated the feasibility of estimating smolt survival and passage probabilities using radiotelemetry data.  Developed longitudinal statistical analyses to analyze time-varying covariates in smolt survival studies.

1999:  Develop a user-specified model development tool that permits investigators to create likelihood models tailored to their evolving research needs.   The model development tool will be extremely valuable in implementing radiotelemetry survival studies where fixed detection locations no longer exist but where antenna arrays can be placed in an unending number of configurations.

2000:  Released upgraded version of Program SURPH.2.  The new program has improved modeling capabilities along with the automatic ability to test model assumptions and produce more reliable confidence interval estimates.  The new version is particularly suited to the paired release-recapture studies ongoing in the Mid-Columbia and Lower Columbia reaches.

2001:  The user's manual for Program SURPH.2 was completed.  In addition, a User Specified Estimation Route Program (USER.1) was developed that provides an extremely flexible and user-friendly environment to create statistical models for the analysis of both juvenile and adult salmonid survival studies.  Program USER.1 is extremely valuable in the design and analysis of the wide variety of radio-tag and acoustic-tag applications currently planned in the Columbia Basin.  The project also assisted NMFS and PSMFC in the evaluation of adult ladder PIT-tag detection facilities at Bonneville Dam.  The project developed statistical models for estimating detection probabilities at that site that will have wider application as additional adult facilities are installed elsewhere in the river.

2002:  The software program User Specified Estimation Route Program was expanded to USER.2.  The new program computes profile likelihood confidence intervals for complex functions of parameters.  This feature is particularly useful in estimating joint survival processes through hydro projects or estimating pool and dam passage survival.  New sample size programs were developed to design single-release, paired-release, and transport-inriver survival studies (i.e., Program SampleSize 1.0).  Program PitPro 1.0 was developed to improve capabilities to construct data files for survival analysis from PTAGIS.  New capabilities include extracting capture histories for both juvenile and adult survival studies.

2003:  Major efforts this year included the development of paper and electronic user manuals for all the major software packages (i.e., SURPH 2.1, USER 2.1, PitPro 1.0, and SampleSize 1.0). With more people using the software, error debugging became important as users tested the limits of the software capabilities.  Improved data entry capabilities were added to Program SURPH 2.1.  

2004:  Diagnostic and graphical tools were added to Program USER to improve interpretation of fitted models.  Program SampleSize was expanded to include replicate releases for the estimation of mean survival.  The most significant accomplishment was the development of a new first-generation program called ROSTER (River Ocean Survival and Transportation Estimation Routine) to provide joint juvenile-to-adult PIT-tag survival analyses.

2005:  Alternative statistical models were developed that could analyze the complex adult radiotelemetry data collected by the US Army Corps of Engineers and the University of Idaho.  The models permit estimation of upriver survival, taking into account fallbacks and straying.  These improved models should help identify more of the "unaccountable loss" and provide confidence bounds on the estimates of adult passage.  Program ROSTER will be made available by the end of 2005.  The program will provide estimates of downriver smolt survival, ocean survival, upriver adult survival, smolt-to-adult ratios, transport-inriver effects, and delayed mortality from PIT-tag releases.

2006:  Program ROSTER (River Ocean Survival and Transportation Estimation Routine) 1.3a became operational with numerous performance measures estimated from the model.  Three technical reports were issued; one on the proper deployment of hydrophone arrays at the mouth of the Columbia River to estimate movement and survival of smolts from the estuary to the continental shelf, and the other, on the estimation of transportation on fall Chinook salmon based on the analysis of PIT-tag data; and a third technical review of marking techniques for salmonid fry and release-recapture methods for estimating fry survival.

2007:  Program PitPro 4.0 was released and greatly improves the joint handling of juvenile and adult PIT-tag detections.  The software also accounts for unpublished anomalies associated with the smolt transport program (e.g., transport bypass events) which could bias PIT-tag estimates if not taken into account.  Program ROSTER 2.0 was updated with additional summary statistics on transport effects and delayed mortality.  A "wiki" site was established so that PIT-tag investigators could share information on tag anomalies and better approaches to data analyses.

2008:  ROSTER analyses were adapted and applied to wild Chinook salmon and steelhead stocks in the Snake River.  A new version of Program USER, 4.1, was released with major improvements in analytical capability and ease of use.  A beta version of SURPH, 3.0, was developed to accommodate current changes in computer operating systems and extend the computing to a dynamic, multi-windows environment to improve the use and clarity of the analyses.  

2009:  Programs SURPH 3.0.and SampleSize 2.0 were completed and released.  A thorough statistical review of adult salmon escapement estimation techniques was completed, including recommendations for improving estimates.  A multi-state migration model for radiotelemetry was developed to model adult upriver migration in the presence of fallbacks at dams and straying into tributaries.  This multi-state model can be adapted to analyze adult PIT-tag data when tributary detection systems come online.  

2010: Program ATLAS (Active Tag Live Adjusted Survival) was developed and released.   This program allows tag life data to be modeled and the results incorporated into the analysis of survival studies using active tags (i.e. radio and acoustic tags).  The result is tag-life adjusted estimates of survival for single release, paired release, and virtual/paired-release study designs.  Also, a peer-reviewed paper was published on release-recapture techniques to be use at federal hydroprojects to assess compliance with BiOp and Fish Accord standards.

2011:  Program ATLAS was upgraded to include estimates of cumulative downriver survival, allow for multiple tag-life corrections for different tag lots, and batch programming.

2012:  Program ATLAS was expanded to permit analyses with and without tag-life corrections.  Program SURPH was updated to include profile confidence intervals.  New user’s manuals released for Programs ATLAS and SURPH.  A beta version of Program TribPit was released capable of analyzing multi-year outmigration of salmonid cohorts to estimate overall in-tributary survivals.

2013:  Program TribPit was developed and released to analyze multiyear outmigration performance of subyearling Chinook salmon and steelhead based on PIT-tag detections in the tributaries.  A prototype software program was developed (i.e., Program BRANCH) to produce complex multistate release-recapture models for the analyses of juvenile and adult migration data based on GUI drawn schematics of the study design.

2014:  Program BRANCH was developed to allow investigators to design and analyze complex smolt and adult movement studies using a graphical interface.  A schematic of the study is converted automatically into statistical software for tag analyses by Program BRANCH.

2015:  Program TribPit SampleSize was developed and released to provide guidance on sample sizes for PIT-tagged juvenile salmonids in tributary survival studies.  The initial version of Program BRANCH also was released to the public.

2016:  Program TribPit 2.0 was developed at the request of regional users.  This version of TribPit allows the simultaneous analysis of multiple releases in a tributary system, thereby improving both precision and breadth of information.

2017:  Program Basin TribPIT was developed and released for cohort analysis of juvenile salmonid movement and survival in tributaries within river basins.  By using multiple releases within the same basin, sample size is increased, thereby improving precision of cohort survival estimates.