All PIT Tag Tools created by PNAMP and/or related to other PNAMP projects, meetings, and workshops can be accessed from this tools table.
| Objective purpose | Species | Target life stage | Description | Reference link | hf:tax:pittag_category |
|---|---|---|---|---|---|
| Failure-time models, tag-life models | JR Skalski, SL Whitlock. 2020. Vitality models found useful in modeling tag-failure times in acoustic-tag survival studies | doi.org/10.1186/s40317-020-00213-z | all publications | ||
| Parameter estimation | AC Pope, JR Skalski, T Lockhard, RA Buchanan. 2016. Generation of multistate release-recapture models using a graphic user interface (GUI) | doi.org/10.1186/s40317-016-0115-6 | all publications | ||
| Marking methods | JR Skalski, RA Buchanan, J Griswold. 2009. Review of marking methods and release-recapture designs for estimating the survival of very small fish: examples from the assessment of salmonid fry survival | dx.doi.org/10.1080/10641260902752199 | all publications | ||
| Abundance | JR Skalski, JJ Millspaugh. 2006. Application of multidimensional change-in-ratio methods using Program USER | www.jstor.org/stable/3785144?origin=JSTOR-pdf | all publications | ||
| Cleaning data, Predation | RA Buchanan, SL Whitlock. 2022. Diagnosing predated tags in telemetry survival studies of migratory fishes in river systems. | doi.org/10.1186/s40317-022-00283-1 | all publications | ||
| all publications | |||||
| Survival, covariate effects | Smith, SG. 1991. Assessing hazards in wild populations using auxiliary variables in tag-release models | http://University of Washington, Seattle, Washington, USA/ | all publications | ||
| Survival, SAR, TIR | RA Buchanan. 2005. Release-recapture models for migrating juvenile and adult salmon in the Columbia and Snake Rivers using PIT-tag and radiotelemetry data | http://University of Washington, Seattle, Washington, USA/ | all publications | ||
| Survival, SAR, TIR | RA Buchanan, JR Skalski. 2007. A migratory life-cycle release-recapture model for salmonid PIT-tag investigations | dx.doi.org/10.1198/108571107X229331 | all publications | ||
| Survival, SAR, TIR | RA Buchanan, JR Skalski, SG Smith. 2006. Estimating the effects of smolt transportation from different vantage points and management perspectives | dx.doi.org/10.1577/M05-080.1 | all publications | ||
| Survival, SAR, TIR | RA Buchanan, JR Skalski, G Mackey, C Snow, AR Murdoch. 2015. Estimating cohort survival through tributaries for salmonid populations with variabl ages at migration | doi.org/10.1080/02755947.2015.1064837 | all publications | ||
| Cohort survival | AB Lowther, JR Skalski. 1998. A multinomial likelihood model for estimated survival probabilities and overwintering for fall Chinook salmon using release-recapture methods | www.jstor.org/stable/1400652 | all publications | ||
| Parameter estimation | JR Skalski, AG Seaburg, RA Buchanan. 2013. The effects of high detection probabilities on model selection in paired release-recapture studies in the era of electronic tagging studies | doi.org/10.1186/2050-3385-1-12 | all publications | ||
| Dam passage survival | R Harnish, JR Skalski, RL Townsend, K Ham. 2020. In serach of a cost-effective approach for estimating dam passage survival | dx.doi.org/10.1002/nafm.10448 | all publications | ||
| Dam passage survival | JR Skalski, RL Townsend, TW Steig, S Hemstrom. 2010. Comparison of two alternative approaches for estimating dam passage survival of salmon smolts | dx.doi.org/10.1577/M09-103.1 | all publications | ||
| Survival | JR Skalski, J Griswold. 2006. A summary of methods for conducting salmonid fry mark-recapture studies for estimating survival in tributaries. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin Vol XXI | pisces.bpa.gov/release/documents/documentviewer.aspx?doc=00025091-2 | all publications | ||
| Survival | WH Pearson, JR Skalski, KL Sobocinski, MC Miller, GE Johnson, GD Williams, JA Southard, RA Buchanan. 2006. A Study of stranding of juvenile salmon by ship wakes along the Lower Columbia River using a before-and-after design: Before-phase results | http://PNNL-15400 2006/1/31 | all publications | ||
| Survival | JR Skalski, RL Townsend, J Lady, AE Giorgi, JR Stevenson, RD McDonald. 2002. Estimating route-specific passage and survival probabilities at a hydroelectric project from smolt radiotelemetry studies | dx.doi.org/10.1139/F02-094 | all publications | ||
| Survival | JR Skalski, MB Eppard, GR Ploskey, MA Weiland, TJ Carlson, RL Townsend. 2014. Assessment of subyearling Chinook Salmon survival through the federal hydropower projects in the main-stem Columbia River | doi.org/10.1080/02755947.2014.910577 | all publications | ||
| Survival | RL Townsend, JR Skalski, P Dillingham, TW Steig. 2006. Correcting bias in survival estimation resulting from tag failure in acoustic and radiotelemetry studies | dx.doi.org/10.1198/108571106X111323 | all publications | ||
| Survival | JR Skalski, RA Buchanan, RL Townsend, TW Steig, S Hemstrom. 2009. A multiple-release model to estimate route-specific and dam passage survival at a hydroelectric project | dx.doi.org/10.1577/M07-227.1 | all publications | ||
| Survival | JR Skalski, SG Smith, RN Iwamoto, JG Williams, A Hoffmann. 1998. Use of passive integrated transponder tags to estimate survival of migrant juvenile salmonids in the Snak and Columbia rivers | dx.doi.org/10.1139/cjfas-55-6-1484 | all publications | ||
| Ascent and fallback statistics at adult fishway ladders | Chinook, Coho, Steelhead, Sockeye | Adult | Seasonal and daily ascent and fallback calculations for PTAGIS observations for user-selected fishway ladder, species, run, rear type, year, release, transportation status. Output: plot, HTML table, CSV. Tool supported by DART. | www.cbr.washington.edu/dart/query/pitadult_fallback | all analyzing-data |
| Adult returns conversion rates pooled by detection year | Chinook, Coho, Steelhead, Sockeye | Adult | Conversion rates calculated for PTAGIS adult life stage observation data aggregated by user-selected release and other attributes including tranportation or in-river. Output: plot, HTML table, additional detail queries. | www.cbr.washington.edu/dart/query/pitadult_conrate | all analyzing-data |
| Data processing | Chinook, Steelhead | Juvenile | Converts valid acoustic-tag detection events into detection history format suitable as input file for survival analysis by ATLAS or other third-party software. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/tagproapp | all analyzing-data |
| Cleaning data, predation | All | Juvenile | Diagnose transferal of tag from study fish to predator in active tagging studies. Tailored to Sacramento-San Joaquin River Delta (California). Tool supported by DART. | www.cbr.washington.edu/analysis/apps/tagpredation | all analyzing-data |
| Detailed detection and release information by tag | Chinook, Coho, Steelhead, Sockeye | Juvenile, Adult | PTAGIS observation and release information by tag for user-selected location, species, run, rear type, observation year. Output: HTML table, CSV. Provides API. Tool supported by DART. Tool supported by DART. | www.cbr.washington.edu/dart/query/pit_obs_detail | all data-access-and-summaries-dart-tools |
| Release basin (HUC4) summary of fish detected at a single location with migration timing | Chinook, Coho, Steelhead, Sockeye | Juvenile, Adult | PTAGIS observation and release information aggregated by year, detection location, species and life stage. Output: HTML table, CSV. Provides API. Tool supported by DART. | www.cbr.washington.edu/dart/query/pit_obs_sum | all data-access-and-summaries-dart-tools |
| Annual summary adult return counts for fish ladders and subbasins by species, run, rear type | Chinook, Coho, Steelhead, Sockeye | Adult | PTAGIS adult life stage observation data aggregated by year for species, run, rear type. Output: HTML table, CSV. | www.cbr.washington.edu/dart/query/pitadult_basin_sum | all data-access-and-summaries-dart-tools |
| Daily summary counts by detection location specific to adult life stage | Chinook, Coho, Steelhead, Sockeye | Adult | PTAGIS adult life stage observation data aggregated by day for user-selected location, species, run, rear type, year. Output: plot, CSV. Provides API. Tool supported by DART. | www.cbr.washington.edu/dart/query/pitadult_graph_text | all data-access-and-summaries-dart-tools |
| ESU / DPS populations migration timing for multiple years for across year comparison | Chinook, Coho, Steelhead, Sockeye | Juvenile, Adult | ESU / DPS populations as identified by DART from PTAGIS release information calculated migration timing and characterists for multiple historical years at a single location. Output: plot, HTML table, CSV. Tool supported by DART. | www.cbr.washington.edu/dart/query/esu_hrt | all run-timing-and-forecasting |
| ESU / DPS summary counts and migration timing for each component stock | Chinook, Coho, Steelhead, Sockeye | Juvenile, Adult | Component stock detection history and migration timing based on user-selected year and life stage for ESU / DPS populations as identified by DART from PTAGIS release information. Output: HTML table and CSV. Provides API. Tool supported by DART. | www.cbr.washington.edu/dart/query/esu_year_sum | all run-timing-and-forecasting |
| Migration timing for multiple year for across years comparison | Chinook, Coho, Steelhead, Sockeye | Adult | PTAGIS observation data aggregated by user-selected population (species, run, rear type, release location) for multiple historical years at a single location. Output: plot, HTML table, CSV.Tool supported by DART. | www.cbr.washington.edu/dart/query/pitadult_hrt | all run-timing-and-forecasting |
| Migration timing for multiple years for across year comparison | Chinook, Coho, Steelhead, Sockeye | Juvenile | PTAGIS observation data aggregated by user-selected population (species, run, rear type, release location) for multiple historical years at a single location. Output: plot, HTML table, CSV. Tool supported by DART. | www.cbr.washington.edu/dart/query/pit_obs_hrt | all run-timing-and-forecasting |
| Failure-time models, Tag-life models | All | Juvenile, Adult | A software package for fitting and comparing failure-time models within the R software environment. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/failcompare | all parameter-estimation-and-custom-modeling |
| Parameter estimation | All | Juvenile, Ocean, Adult | Implements USER from command line and performs multiple estimation runs from a batch file without user intervention between runs. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/userconsole | all parameter-estimation-and-custom-modeling |
| Parameter estimation | All | Juvenile, Ocean, Adult | Graphical creation of custom survival models for tagging data, allows for multistate structure. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/branch | all parameter-estimation-and-custom-modeling |
| Sample size | All | All | A suite of sample size programs for estimating parameters from various release-recapture models: Single Release, Paired Release, Virtual Paired Release, Ricker Two-Release, ViRDCt full model, and ViRDCt reduced model. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/samplesize | all sample-size-and-study-design |
| Sample size | Chinook, Steelhead | Juvenile | Tool for sample size calculations for tributary cohort survival studies. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/TribPitSampleSize | all sample-size-and-study-design |
| Study design: sample size | Chinook, Steelhead | Juvenile | Tool for sample size calculations for tributary survival studies. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/TribPitSampleSize | all sample-size-and-study-design |
| Cohort survival, Age composition | Chinook, Steelhead | Juvenile | Estimates reach-specific survival from tributaries to mainstem, accounts for variable age at migration. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/BasinTribPit | all survival-and-travel-time-modeling |
| ESU / DPS harmonic mean single- and multiple-reach travel times for 2002 to present for comparing population-level travel times across years | Chinook, Coho, Steelhead, Sockeye | Juvenile, Adult | ESU / DPS populations as identified by DART from PTAGIS release information calculated harmonic reach travel times with SE and Count for years 2002 to present. Output: HTML table and daily plot. Tool supported by DART. | www.cbr.washington.edu/dart/query/esu_tt | all survival-and-travel-time-modeling |
| Mean reach travel time calculations both arithmetic and harmonic | Chinook, Coho, Steelhead, Sockeye | Adult | User-selected population based on release and observation information with mean reach travel time calculations for PTAGIS adult life stage. Output: HTML table with results via email. Tool supported by DART. | www.cbr.washington.edu/dart/query/pitadult_tt | all survival-and-travel-time-modeling |
| Survival | Chinook, Steelhead | Juvenile | Estimation of juvenile outmigration survival from tributaries to mainstem river using PIT tags. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/tribPit | all survival-and-travel-time-modeling |
| Survival | All | Juvenile, Adult | Implements Program ATLAS in the R environment. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/cbratlas | all survival-and-travel-time-modeling |
| Survival | Chinook, Coho, Steelhead, Chum | Adult | Estimates mortality during rock blasting operations. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/blasttake | all survival-and-travel-time-modeling |
| Survival | All | Juvenile, Adult | Models survival and detection probability in relation to environmental and experimental effects. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/surph | all survival-and-travel-time-modeling |
| Survival through reach, past dam | All | Juvenile, Adult | Estimates survival from tagging data from various study designs; accounts for premature tag failure or tag loss. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/atlas | all survival-and-travel-time-modeling |
| all survival-and-travel-time-modeling | |||||
| Cleaning data | All | Juvenile, Ocean, Adult | Filters out noise from acoustic-tag receiver data. Designed to use receptions of acoustic signals from JSATS tags on cabled and autonomous hydrophone nodes. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/fast | all analyzing-data |
| ESU / DPS populations smolt-to-adult return (SAR) survival calculations | Chinook, Coho, Steelhead, Sockeye | Juvenile, Ocean, Adult | ESU / DPS populations as identified by DART from PTAGIS release information calculated smolt-to-adult return (SAR) survival calculations with user-configurable options for analysis reach and transportation status. Output: plot, HTML table, CSV. Tool suppo | www.cbr.washington.edu/dart/query/pit_sar_esu | all smolt-to-adult-return-sar |
| Daily summary counts by detection location | Chinook, Coho, Steelhead, Sockeye | Juvenile, Adult | PTAGIS observation data aggregated by day for user-selected location, species, run, rear type, year. Output: plot, CSV. Provides API. Tool supported by DART. | www.cbr.washington.edu/dart/query/pit_obs_graph_text | all data-access-and-summaries-dart-tools |
| Run-timing predictions | Chinook, Coho, Steelhead, Sockeye | Juvenile | Uses real-time information about the current status of various Columbia Basin juvenile salmon runs along with current hydrographic information to predict the future progress of migrating fish. Tool supported by DART. | www.cbr.washington.edu/inseason/smolt_snake_pit | all run-timing-and-forecasting |
| Parameter estimation | All | Juvenile, Ocean, Adult | Flexible tool to develop statistical models for tagging and counts data. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/user | all parameter-estimation-and-custom-modeling |
| Study design: sample size | All | Juvenile, Ocean, Adult | Calculates optimal sample size to obtain desired study precision for fish and wildlife studies using release-recapture methods. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/samplesize | all sample-size-and-study-design |
| Survival, Process PTAGIS data, Travel time | Chinook, Coho, Steelhead, Sockeye, Chum | Juvenile, Adult | Cleans and converts PTAGIS observation data into capture histories for programs SURPH, ROSTER. Fits CJS model, estimates travel time. Tool supported by DART. | www.cbr.washington.edu/analysis/apps/pitpro | all survival-and-travel-time-modeling |