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@CefasRepRes Centre for Environment Fisheries and Aquaculture Science (Cefas)

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    74 repositories

    • FUME

      Public
      Calculates the Forel-Ule Index of water quality from surface reflectances. Works with point and image data.
      Jupyter Notebook
      •
      Other
      •6•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • MixME

      Public
      R package for Mixed-fishery Multi-stock Evaluation
      R
      •0•0•4•0•Updated Aug 8, 2025Aug 8, 2025

    • aquanet-mod

      Public
      R scripts for AquaNet-Mod (The Aquaculture Disease Network Model).
      R
      •
      Other
      •0•1•2•0•Updated Aug 8, 2025Aug 8, 2025

    • aquanet

      Public
      R package containing the functions required to run AquaNet-Mod (The Aquaculture Disease Network Model).
      r-package
      R
      •
      Other
      •0•2•0•0•Updated Aug 8, 2025Aug 8, 2025

    • gene-pools-paper

      Public
      Pre-processing scripts for manuscript for gene pools project.
      0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • NEMO4.0-FABM

      Public
      Fortran
      •
      Other
      •1•1•2•0•Updated Jul 18, 2025Jul 18, 2025

    • CO_AMM15

      Public
      Coastal Ocean (CO) configuration of the Atlantic Margin Model (1.5 km resolution)
      Fortran
      •1•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • CO_AMM7

      Public
      AMM7 configuration for testing various vertical coordinate options
      Fortran
      •2•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • eDNA-spatial-bound-paper

      Public
      Code used in Silva et al 2025. Frontiers in Marine Science. Modelling the spatial bound of an eDNA signal in the marine environment – the effect of local conditions.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • TawTorridgeCatchmentData

      Public
      Data repository for SWAT model catchment data from the Taw and Torridge catchments
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 4, 2025Jul 4, 2025

    • agriforwards-summer-school-2022

      Public
      Planning for the UEA / Cefas AgriFoRwArdS summer school 2022
      Jupyter Notebook
      •9•7•0•1•Updated Jul 3, 2025Jul 3, 2025

    • cefas-pi-10-edge-ai

      Public
      Edge AI system used on board the Cefas Endeavour for plankton inference
      Python
      •
      Other
      •0•0•1•0•Updated Jul 1, 2025Jul 1, 2025

    • ICES-VMS-and-Logbook-Data-Call_Cefas

      Public
      repository for repsonse to ICES VMS& LOGBOOK DATACALL adapated to Cefas requirements
      R
      •
      GNU General Public License v3.0
      •5•0•12•0•Updated Jul 1, 2025Jul 1, 2025

    • salmon-rod-exploitation

      Public
      Article and analysis code for ICES JMS paper "Estimation of returning Atlantic salmon stock from rod exploitation rate for principal salmon rivers in England & Wales"
      R
      •
      Other
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • flowcytometertool

      Public
      Python
      •
      Other
      •0•2•20•0•Updated Jun 23, 2025Jun 23, 2025

    • Cefas_UEA_RCourse2025

      Public
      Repo for the Cefas UEA R Course
      R
      •
      Other
      •2•0•0•0•Updated Jun 17, 2025Jun 17, 2025

    • shipwreck-oil-detection-colab

      Public
      Google Colab tool for detecting oil spills from historical shipwrecks
      Jupyter Notebook
      •
      MIT License
      •0•0•3•0•Updated Jun 12, 2025Jun 12, 2025

    • ices_vms_logbook_datacall

      Public
      Code to produce the datasets required for the annual ICES VMS/Logbook datacall
      R
      •0•1•2•1•Updated Jun 10, 2025Jun 10, 2025

    • cefasMOS

      Public
      R
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • mizerShiny

      Public
      mizerShiny is a frontend to mizer models that allows interactive simulation of mizer models.
      R
      •
      MIT License
      •2•0•0•0•Updated Jun 5, 2025Jun 5, 2025

    • SHG_loggerManagerApp

      Public
      Shiny application for the management of HOBO V2, MX and miniDOT data loggers
      R
      •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • GeoFISH_DCG

      Public
      GeoFISH Data Coordination Group repository . GeoFISH UK high-resolution fishing activity methods documentation and share with experts and wider audience .
      0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • Git_Training

      Public
      ssmod
      HTML
      •1•5•0•0•Updated May 16, 2025May 16, 2025

    • MetOffice_CTD_send

      Public
      Automated CTD send from a research vessel
      C
      •2•0•0•0•Updated May 1, 2025May 1, 2025

    • uk-fvcom

      Public
      Fortran
      •12•0•0•0•Updated May 1, 2025May 1, 2025

    • HistoryMatchingMSE

      Public
      This runs the code to accompany the paper "Using history matching to speed up Management Strategy Evaluation grid searches" by Michael A. Spence currently under review at the Canadian Journal of Fisheries and Aquatic Sciences.
      R
      •
      Other
      •0•0•0•0•Updated Apr 23, 2025Apr 23, 2025

    • BayOfBengal_ParticleTracking_paper

      Public
      Code used to run and post-process OceanParcels particle tracking simulations in the Bay of Bengal for a paper submitted to Ocean Science.
      Jupyter Notebook
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • EMODnet-Biology-products-erddap-demo

      Public
      Use R to turn a data frame with biological dataset into a four dimensional array and save in a NetCDF file.
      R
      •
      MIT License
      •1•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • EcoEnsemble

      Public
      R package for implementing the ensemble framework for combining ecosystem models.
      C++
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Mar 19, 2025Mar 19, 2025

    • cefasRBR

      Public
      R package for working with RBR Profiling instruments
      R
      •
      MIT License
      •0•0•0•0•Updated Feb 24, 2025Feb 24, 2025