Contract Description:

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 Program TribPit, to analyze the complex PIT-tag data collected during juvenile outmigration in the headwaters. Program SampleSize was developed to assist investigators in the design of single-release, paired-release, transport-inriver, balloon-tag, and acoustic-tag survival studies. Program Tributary Survival SampleSize was developed to help investigators determine tag-release sizes for juvenile studies in the tributaries. Program Basin TribPit was developed to simultaneously analyze multiple headwater releases within a river basin. Program BRANCH was developed to analyze the complex movements of smolts and adults in tributaries or estuarine environments. Recent endeavors have included development of R packages to make our software more accessible to the newer generations of fisheries scientists, including the ‘failCompare’ package, which aids users in fitting and selecting failure time models such as those used in active tag studies, and an R package version of Program Atlas. Technical support is provided to investigators through instruction, consultation, and assistance in the design and analysis of complex datasets. Each year, this project assists investigators in the design and analysis of multiple 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 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 and lamprey 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, steelhead, sockeye, and coho during smolt outmigration, and lamprey during migration, 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, software instructional videos, 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 (1993–2021). 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 and alternative spill operations 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), adult returns (SARs), and delayed mortality (D).
12.    Detection rates of juvenile and adult PIT-tag facilities.
13.    Estimation of adult salmon overshoot rates and fallback rates by project and fish stock.
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.    Estimates of juvenile cohort survival migrating out of tributaries.
20.    Escapement estimates of adult steelhead to Upper Columbia Basin tributaries.
21.    Historical trends in PIT-tag release and detection counts at FCRPS dams and in the Columbia River estuary.
22.    Prototype assessment of tributary PIT-tag detection needs for estimation of SAR, adult distribution, adult escapement, and juvenile emigration success.
23.    Contribution to BPA PIT Plan strategy document.

These data have influenced the choices of current mitigation practices and strategies for future hydro-operations.

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 1999–2018, 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]). A subsequent decade of analyses confirm the significant effect of ocean conditions on salmonid returns.

Over the years 2010–2014 and 2018, 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. The former 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 Tributary Survival 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 and subyearling Chinook salmon 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.

In 2018, this project updated and released a new version of Program SampleSize. The project also developed the statistical models to assess bycatch mortality of wild salmonids caught in an experimental commercial fish trap on the Columbia River.

In 2018–2019, the ViRDCt (Virtual Release with Dead Fish Correction) model was developed to provide a more cost-effective means of estimating dam passage survival. Also developed was an interactive program for Sample Size calculations using this new tag-release model.

In 2020, instructional videos were produced for programs PitPro, Basin TribPit, Branch, and Program SampleSize. An instructional workshop was provided to researchers from IDFG, WDFW, ODFW, and PSMFC in Program Basin TribPit and Program Tributary Survival SampleSize. Methods were developed to estimate the take of adult coho from underwater rock blasting. A comprehensive review of over 40 tag-life studies from acoustic telemetry studies from 2002–2018 was performed to provide guidance to researchers on how best to incorporate premature tag failure into survival analysis from active-tag studies. Analysis was provided on the impacts of the new spillway detector at Lower Granite on estimation of survival to Lower Granite and in the hydrosystem, the potential impacts to survival estimation of PIT-tagging restrictions due to COVID-19, and the impact on hydrosystem survival estimation of ending PIT-tag monitoring in the estuary (i.e., estimating survival only to John Day instead of to Bonneville). Study design considerations were provided on a study of new turbine passage at Ice Harbor Dam anticipated to occur in 2022.

In 2021, analytical software was developed as an R package to both fit and compare multiple statistical models of tag failure, a necessary component of active tag studies. An R package was developed for Program Atlas to meet the analysis needs of researchers who prefer using R over a desktop application. Analysis was provided on where to focus PIT-tag detection efforts at new and expanded sites downstream of Bonneville (Columbia River estuary).

In 2022, the analysis of historical trends in annual release and detection numbers of PIT-tagged smolts at key sites in the FCRPS was finalized and a draft manuscript is in preparation. A prototype assessment was developed of tributary PIT-tag detection needs for estimation of SAR, adult distribution, adult escapement, and juvenile emigration success, using Wenatchee River Basin Spring Chinook Salmon as a model. High level guidance was contributed as part of the BPA PIT Plan strategy document.

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. 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., SampleSize, SURPH, USER, TribPit, ROSTER, ATLAS, BRANCH, ViRDCt, and Basin TribPit) that are accessible to the Columbia Basin fisheries community via the internet (http://www.cbr.washington.edu/analysis.html). Development of software packages for the R statistical computing platform began in 2021. Additional products include user's manuals, software for sample size calculations (i.e., SampleSize 3.2), instructional videos, 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. A 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 current generation of Program SURPH was released in 2013 and includes detection-only modeling and a simpler form of input files for greater ease of use. The software for Program SampleSize was expanded to include the Virtual with Paired Release model design in 2013, 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 1.4 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 Program Basin TribPit to allow juvenile PIT-tag data within entire river basins to be analyzed simultaneously to improve the precision of juvenile tagging studies. In 2018, an updated and expanded version of Program SampleSize was released, and the Full and Reduced ViRDCt models were added in 2019 (version 3.2). In 2019, a substantial effort to produce instructional videos for all our statistical software began; this effort continued in 2020, 2021, and 2022. These instructional videos assist users and reduce the need and cost for training sessions. Starting in 2021 and continuing in 2022, Program BRANCH was updated to provide greater ease of use in data loading, model fitting, and reporting of results, and Program USER was expanded for greater ease of use within with other software (e.g., Program BRANCH or the R computing environment). Also in 2021, an initiative began to develop R packages of our software to meet the computing needs of more researchers, including an R package version of Program ATLAS (“cbrATLAS 0.0.1.3”; Single Release model) and an R package (“failCompare”), designed to help users fit and select among competing survival models for failure time data such as arise from tag-life studies of active tags.  A second initiative began in 2021 to upgrade existing software programs to use modern software libraries to make them more robust and meet the security needs of our users. As part of this initiative, Program SURPH was upgraded in 2021, and programs PitPro and ATLAS were upgraded in 2022. Additionally, starting in 2021 and completed in 2022, Program ATLAS was expanded (version 1.8) to include the Full ViRDCt (Virtual Release with Dead Fish Correction) model designed to provide a more cost-effective means of estimating dam passage survival; the Reduced ViRDCt model was also added in 2022. Also in 2022, the Paired Release model was added to the R version of ATLAS, and failCompare was expanded to provide more informative error messaging and increased model-fitting ability.

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.

2018: An expanded and revised version of Program SampleSize was released.

2019: Program ViRDCt was developed to both design (i.e., sample size calculations) and analyze virtual releases with dead fish correction to provide a more cost-effective approach to estimating dam passage survival. Also, extensive efforts to develop instructional videos to accompany our statistical software began (i.e., instructional videos for five software programs completed).

2020: Instructional videos were developed for three more software programs, and an additional video performed for the ViRDCt model component of Program SampleSize. An instructional workshop on Programs Basin TribPit and Tributary Survival SampleSize was conducted in Lewiston, ID.

2021: Additional instructional videos were produced for programs Basin TribPit, Branch, SURPH, and USER. Analytical software was developed as an R package to both fit and compare multiple statistical models of tag failure, a necessary component of active tag studies. An R package was developed for Program Atlas to meet the analysis needs of researchers who prefer using R over a desktop application. Program Branch was extended to meet user needs on data loading, model fitting, and reporting. Program SURPH was updated to use modern software libraries.

2022: A full series of instructional videos were produced for Program ROSTER, and additional instructional videos were produced for programs ATLAS and SURPH. Programs PitPro and ATLAS were upgraded to use modern software libraries, and additional options were added to Program BRANCH. Both the Full ViRDCt model and the Reduced ViRDCt model were added to the desktop application version of Program ATLAS. The Paired Release model was added to the R version of ATLAS (“cbrATLAS”), and improved error handling was added to the R package “failCompare” and Program TagPro. The utility of the console version of Program USER was expanded for easier use in other software packages.