Tools & Models

Fish Growth & Vitality

  • Egg Growth of Pre-emergent Salmon -- The on-line egg growth model tracks egg development from spawning to emergence, and then uses a bioenergetics to model the growth of fry after emergence during their first season of growth. It is useful for examining the role of seasonal temperatures on early life development and growth.
  • Vitality Model -- The vitality-based survival model is a parametric model for relating stressors and environmental properties to organism survivorship. The web page includes research papers, S-PLUS code, sample data file, and documentation.

Fish Passage

  • COMPASS Comprehensive Passage Model -- COMPASS model is being developed by scientists from throughout the Pacific Northwest, led by NOAA. The purpose of the model is to predict the effects of alternative operations of Snake and Columbia River dams on salmon survival rates, expressed both within the hydrosystem and latent effects which may occur outside the hydrosystem. The web page includes current applications of the model and documentation.
  • Eulerian-Lagrangian-Agent Method / Evaluating Likely Animal Movement (ELAM) Integrating spatial/cognitive ecology, particle-tracking, and hydraulic/water quality modeling for fisheries engineering & ecohydraulics research -- ELAM is a mechanistic mathematical approach for decoding and forecasting the multi-dimensional movement behavior patterns of individual animals responding to patterns in abiotic and biotic stimuli available to engineering (e.g., hydrodynamic, water quality, eutrophication, GIS, etc.) models or a priori field data.
  • RealTime Forecasters -- The Realtime Forecasters use pattern recognition techniques to predict the percent of the run-to-date and days to a specific percent of the run of juvenile salmonids in the Columbia Basin. The statistical algorithms smooth historical trends in PIT tag arrivals or passage indices and use a generalized weight least squares decision criterion in making predictions.

Parameter Estimation

  • ATLAS (Active Tag-Life-Adjusted Survival) -- Survival estimates from acoustic tag data, corrected for tag-life failure probabilies.
  • Basin TribPit -- Cohort Analysis of Juvenile Salmonid Movement and Survival in Tributaries.
  • BlastTake -- Estimated mortality during rock blasting operations.
  • Branch Visual modeller for mark/recapture studies- used to define custom survival models graphically in order to estimate survival-related parameters.
  • FAST (Filtering Acoustic Signal Tags) -- A program for filter out noise from acoustic tag reception data. The program is designed to work receptions of acoustic signals from JSATS tags on cabled and autonomous hydrophone nodes.
  • PitPro (PIT Tag Processor) -- Includes CaptHist. A program for processing PTAGIS data into capture histories. PitPro has a graphical user interface while CaptHist is a console or command line application.
  • PopRecon (POPulation RECONstruction) -- A program for estimating population abundance based on full age-at-harvest data, supplemented with harvest effort and auxiliary estimates of survival, abundance, or harvest vulnerability.
  • ROSTER (River-Ocean Survival and Transportation Effects Routine) Program ROSTER models the life cycle of Pacific salmonids from the initiation of the juvenile migration as smolts to the end of the spawning migration as adults.
  • SampleSize -- A suite for four sample size programs for estimating parameters: SingleRelease, PairedRelease, PairedRadio, and TransportInRiverRatio. The web page includes the SampleSize executables.
  • SURPH (SURvival under Proportional Hazards) -- SURPH is an analytical tool for estimating survival using release-recapture data as a function of environmental and experimental effects. The web page includes the SURPH executable and documentation.
  • TagProApp Acoustic-Tag Data Translation Utility -- Desktop application which takes valid acoustic-tag events (produced by FAST or equivalent software) and creates an output file of capture/detection histories used for survival analysis by ATLAS or other third-party software.
  • TribPit Analysis of PIT-tag detections in tributaries.
  • Tributary Survival SampleSize Tool for sample size calculations for tributary survival studies.
  • USER (User Specified Estimation Routine) -- The program USER is a flexible software tool that allows investigators to develop statistical models for analyzing tagging and counts data. The web page includes the USER executable and documentation.

Past Projects & Programs

  • Coast Model -- The Coast Model is a code framework that can be configured at runtime to represent many different models depending upon the specific process algorithms and data specified in the input files. Currently, the Coast Model only contains algorithms used by the Pacific Salmon Commission (PSC) chinook model. The web page includes the Coast Model executable, data files, documentation, and source code.
  • CRiSP Harvest (Chinook Salmon Harvesting Model) -- CRiSP Harvest model simulates the harvest of 30 chinook salmon stocks by 25 fisheries over an extended time horizon. The geographic range covered by the model extends from Southeast Alaska to the Oregon coast. The web page includes the CRiSP Harvest executable and documentation.
  • CRiSP Passage (Columbia River Salmon Passage Model) -- Actively developed and used from 1988 through 2006. CRiSP Passage model predicts downstream migration and survival of individual juvenile salmonid stocks from the tributaries and dams of the Columbia and Snake rivers to the estuary. It is also stochastic, incorporating measures of variability and uncertainty into survival predictions. The web page includes the CRiSP Passage executable, data files, and documentation.
  • Dissolved Gas Modeling Core Team -- From 1995 through 1997, the Dissolved Gas Modeling Core Team web page coordinated the work of multiple agencies to develop and implement dissolved gas modeling for the major hydroelectric projects in the Columbia Basin.
  • GeoMap for Java - Developed in 1997. Java Mapping System for GIS Data. GeoMap is a collection of Java classes designed to display latitude and longitude coordinate data on an interactive canvas. The tool was written in 1997 and no further development is planned. The web page includes the source code.
  • NMFS Harvest Modeling Project -- From 1996 through 1999, the NMFS Harvest Modeling Project web page coordinated the work of multiple agencies to develop and implement various harvest algorithms including the CRiSP Harvest model, PM Selective Fishery Modeling and Data Retrieval, and the PSC Selective Fishery Simulation Model.
  • Radio Telemetry Survey -- This experimental tool was developed in 1997 to plot juvenile salmon radio telemetry data.