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@SWFSC Southwest Fisheries Science Center

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    52 repositories

    • estimATM

      Public
      A tool for planning, execution, analysis, and reporting of CPS biomass from surveys using the acoustic-trawl method (ATM)
      R
      •
      Apache License 2.0
      •0•3•13•0•Updated Feb 3, 2026Feb 3, 2026

    • MSI-data

      Public
      R
      •0•1•1•0•Updated Jan 27, 2026Jan 27, 2026

    • MSI-report

      Public
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • glider-lab

      Public
      NOAA Fisheries ESD glider lab
      glidersswfsc-esd
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •0•3•47•0•Updated Jan 22, 2026Jan 22, 2026

    • standard-glider-files

      Public
      Standard files that are put on all gliders before deployment
      glidersswfsc-esd
      Mathematica
      •0•0•0•0•Updated Jan 15, 2026Jan 15, 2026

    • SardineRecruitIndex

      Public
      Development of a recruitment index for the northern stock of Pacific sardine
      HTML
      •
      Creative Commons Zero v1.0 Universal
      •2•1•11•0•Updated Jan 15, 2026Jan 15, 2026

    • glider_processing_code

      Public
      US AMLR glider processing code
      acousticsglidersswfsc-esd
      MATLAB
      •1•0•0•0•Updated Dec 23, 2025Dec 23, 2025

    • atmData

      Public
      R
      •
      Creative Commons Zero v1.0 Universal
      •0•1•2•0•Updated Dec 15, 2025Dec 15, 2025

    • atm

      Public
      A collection of functions used to conduct acoustic-trawl method surveys of coastal pelagic fish species (CPS), analyze the data, and report the results.
      R
      •
      Other
      •0•4•3•0•Updated Dec 12, 2025Dec 12, 2025

    • CruzPlot

      Public
      CruzPlot is is a utility program oriented to create maps and plot data from data files in the "DAS" format, typically produced by WinCruz.
      R
      •
      Apache License 2.0
      •1•2•5•0•Updated Oct 1, 2025Oct 1, 2025

    • DGNBycatch

      Public
      0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • amlrian

      Public
      A collection of functions, especially for Shiny apps connected to AMLR databases, used by other AMLR packages
      rus-amlrswfsc-esd-usamlr
      R
      •
      Apache License 2.0
      •0•0•2•0•Updated Sep 25, 2025Sep 25, 2025

    • tamatoamlr

      Public
      R package with associated Shiny app for analyzing and visualizing data from the AERD Pinniped Research Program
      rus-amlrswfsc-esd-usamlr
      R
      •
      Apache License 2.0
      •2•0•7•0•Updated Sep 23, 2025Sep 23, 2025

    • glider-lab-manual

      Public
      Quarto website for ESD glider lab
      glidersswfsc-esd
      Lua
      •
      Creative Commons Zero v1.0 Universal
      •0•2•1•0•Updated Sep 19, 2025Sep 19, 2025

    • swfscAirDAS

      Public
      Functions for processing and analyzing aerial survey DAS data generated by the TURTLE, PHOCOENA, and CARETTA programs at the Southwest Fisheries Science Center
      R
      •
      Apache License 2.0
      •1•0•1•0•Updated Aug 29, 2025Aug 29, 2025

    • ApportionMnStocks

      Public
      Provides stock membership probabilities for U.S. West Coast humpback whales based on photo-identification data
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • FKW_Genome

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • esdglider

      Public
      Utility functions for ESD glider processing
      glidersswfsc-esd
      Jupyter Notebook
      •
      Apache License 2.0
      •1•3•5•0•Updated Aug 20, 2025Aug 20, 2025

    • CMRutils

      Public
      Misc tools for mark-recapture analysis
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • swfscDAS

      Public
      R package for processing and analyzing DAS data
      R
      •
      Apache License 2.0
      •0•4•4•0•Updated Aug 11, 2025Aug 11, 2025

    • ObsCovgTools

      Public
      Estimates minimum fisheries observer coverage required to achieve a specific objective
      R
      •
      Other
      •2•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • sardine_otolith_sampling_analysis

      Public
      This repository contains the data and analysis used in the manuscript on post-survey otolith subsampling strategies on Pacific Sardine by Schwartzkopf et al.
      R
      •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • banter

      Public
      banter is a package for creating hierarchical acoustic event classifiers out of multiple call type detectors.
      machine-learningcranrrandom-forestnoaasupervised-learningclassificationr-packagewhalesacoustics
      HTML
      •1•9•1•0•Updated Jun 17, 2025Jun 17, 2025

    • swfscMisc

      Public
      Collection of utility, analytical, mapping, and plotting functions used at the Southwest Fisheries Science Center.
      R
      •1•0•0•0•Updated Jun 9, 2025Jun 9, 2025

    • cs-phoc

      Public
      Repository for CS-PHOC dataset and data paper
      R
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • ssafs-pup-census

      Public
      South Shetland Antarctic fur seal (SSAFS) total synoptic pup counts
      R
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • Mn-StockProportions-USWC-2025

      Public archive
      Final R scripts and results for 2025 Tech Memo on estimating humpback whale stock proportions by latitude for the U.S. West Coast
      R
      •
      Apache License 2.0
      •1•0•0•0•Updated May 30, 2025May 30, 2025

    • SeriousInjury

      Public
      Classify Whale Injuries as Serious or Non-Serious with Classification Trees. https://www.frontiersin.org/articles/10.3389/fmars.2022.863070
      R
      •
      Other
      •1•2•0•0•Updated May 15, 2025May 15, 2025

    • surveyR

      Public
      A package containing functions used by the Advanced Survey Technologies group at NOAA's Southwest Fisheries Science Center.
      R
      •
      Other
      •0•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • processROV

      Public
      Code for processing ROV data from SWFSC surveys
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 14, 2025Apr 14, 2025