r4ss - R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.24.00-prerel, from July 2025). Support for 3.24 models is only through the core functions for reading output and plotting.

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fisheriesfisheries-stock-assessmentstock-synthesis

11.96 score 47 stars 2 dependents 2.1k scripts 352 downloads

FLCore - Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flrproject.org/>.

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fisheriesflrfisheries-modelling

9.05 score 17 stars 25 dependents 1.2k scripts 9 downloads

icesSAG - Stock Assessment Graphs Database Web Services

R interface to access the web services of the ICES Stock Assessment Graphs database <https://sg.ices.dk>.

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8.12 score 14 stars 4 dependents 130 scripts 753 downloads

ggplotFL - Using ggplot2 in FLR

Using ggplot2 for FLR. Provides (1) overloaded ggplot methods for various FLR classes, (2) ggplot-based versions of standard plots in the FLCore package, and (3) new geoms for using FLR objects.

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visualizationggplot2fisheriesflr

7.89 score 4 stars 14 dependents 622 scripts

FLasher - Projection and Forecasting of Fish Populations, Stocks and Fleets

Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.

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forecastfisheriesflrcpp

7.50 score 2 stars 7 dependents 312 scripts

stockassessment - State-Space Assessment Model

Fitting SAM...

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stockassessmentcpp

7.24 score 52 stars 2 dependents 414 scripts

TAF - Transparent Assessment Framework for Reproducible Research

General framework to organize data, methods, and results used in reproducible scientific analyses. A TAF analysis consists of four scripts (data.R, model.R, output.R, report.R) that are run sequentially. Each script starts by reading files from a previous step and ends with writing out files for the next step. Convenience functions are provided to version control the required data and software, run analyses, clean residues from previous runs, manage files, manipulate tables, and produce figures. With a focus on stability and reproducible analyses, the TAF package comes with no dependencies. TAF forms a base layer for the 'icesTAF' package and other scientific applications.

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7.13 score 3 stars 2 dependents 416 scripts 487 downloads

FLBRP - Reference Points for Fisheries Management

Calculates a range of biological reference points based upon yield per recruit and stock recruit based equilibrium calculations. These include F based reference points like F0.1, FMSY and biomass based reference points like BMSY.

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reference pointsfisheriesflrcpp

6.62 score 2 stars 6 dependents 386 scripts

icesTAF - Functions to Support the ICES Transparent Assessment Framework

Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.

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6.54 score 5 stars 1.2k scripts 369 downloads

icesDatras - DATRAS Trawl Survey Database Web Services

R interface to access the web services of the ICES (International Council for the Exploration of the Sea) DATRAS trawl survey database <https://datras.ices.dk/WebServices/Webservices.aspx>.

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6.43 score 15 stars 150 scripts 228 downloads

spict - Stochastic surplus Production model in Continuous-Time (SPiCT)

Fits a surplus production model to fisheries catch and biomass index data.

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fisheries-managementfisheries-stock-assessmentspictcpp

6.32 score 29 stars 144 scripts

mse - Tools for Running Management Strategy Evaluations using FLR

A set of functions and methods to enable the development and running of Management Strategy Evaluation (MSE) analyses, using the FLR packages and classes and the a4a methods and algorithms.

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simulationmsefisheriesflra4amanagement-strategy-evaluation

6.08 score 4 stars 4 dependents 178 scripts

icesVocab - ICES Vocabularies Database Web Services

R interface to access the Vocabularies REST API of the ICES (International Council for the Exploration of the Sea) Vocabularies database <https://vocab.ices.dk/services/>.

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5.99 score 7 stars 4 dependents 116 scripts 727 downloads

icesAdvice - Functions Related to ICES Advice

A collection of functions that facilitate computational steps related to advice for fisheries management, according to ICES guidelines. These include methods for calculating reference points and model diagnostics.

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5.44 score 7 stars 3 dependents 88 scripts 378 downloads

RDBEScore - Functions for the ICES Regional Database and Estimation System (RDBES)

The RDBEScore package provides functions to import and work with fisheries data downloaded from the ICES RDBES database. It also contains functions to perform estimation analysis using the resulting objects.

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5.39 score 1 stars 42 scripts

ss3diags - Stock Synthesis Model Diagnostics for Intergated Stock Assessments

Compilation of diagnostic functions for Stock Synthesis models, which developed for the manuscript "Using Model Diagnostics in Integrated Stock Assessments".

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stock-synthesis

5.06 score 5 stars 164 scripts

mixfishtools - WGMIXFISH tools for reproducibility

Contains plot templates used in WGMIXFISH-ADVICE and Fisheries Overviews.

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4.73 score 3 stars 8 scripts

icesConnect - Provides User Tokens for Access to ICES Web Services

Provides user tokens for ICES web services that require authentication and authorization. Web services covered by this package are ICES VMS database, the ICES DATSU web services, and the ICES SharePoint site <https://www.ices.dk/data/tools/Pages/WebServices.aspx>.

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4.49 score 9 dependents 23 scripts 426 downloads

msy - Estimation of Equilibrium Reference Points for Fisheries

Methods to estimate equilibrium reference points for fisheries data. Currently data must be converted into FLStock objects of the FLR (Fisheries Library in R) style, defined in the R package FLCore.

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4.18 score 13 stars 58 scripts

icesDatsu - Functions to Interact with the ICES Data Submission Utility (DATSU)

Functions to Interact with the ICES Data Submission Utility (DATSU) <https://datsu.ices.dk/web/index.aspx>.

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4.13 score 3 stars 3 dependents 5 scripts 752 downloads

FLFishery - Classes and Methods for Simpler Fleet/Fishery Modelling

A set of classes and methods for modelling of fleet dynamics. Fisheries are groups of vessels sharing an effort time series, with static or changing spatio-temporal patterns in selectivity.

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fisheriesflr

3.84 score 8 dependents 19 scripts

FLSRTMB - FLSR in TMB

Estimates FLR spawner recruitment relationships in TMB

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stock-recruitfisheriesflrtmbadcpp

3.81 score 1 stars 1 dependents 43 scripts

icesSD - Stock Database Web Services

R interface to access the web services of the ICES Stock Database <https://sd.ices.dk>.

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3.69 score 1 stars 1 dependents 33 scripts 627 downloads

FLRef - Reference point computation for advice rules

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3.55 score 3 stars 39 scripts

icesDatsuQC - Run Quality Checks on Data Prior to Submission to ICES

Run quality checks on data sets using the same checks that are conducted on the ICES Data Submission Utility (DATSU) <https://datsu.ices.dk>.

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3.48 score 2 stars 1 dependents 591 downloads

icesFO - Functions to support the creation of ICES Fisheries Overviews

Functions to support the creation of ICES Fisheries Overviews.

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3.47 score 2 stars 296 scripts

cat3advice - ICES category 3 empirical harvest control rules

A package to apply the the ICES category 3 empirical (model-free) harvest control rules.

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3.32 score 3 stars 14 scripts

icesRDBES - Tools for the ICES Regional DataBase and Estimation System

Tools to support the ICES Regional DataBase and Estimation System (RDBES) <https://sboxrdbesapi.ices.dk/rdbescatalogue/> to access, analyse, and process fisheries data collected under the EU Data Collection Framework.

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2.86 score 1 stars 12 scripts

FLfse - Fisheries Sampling Evaluation In FLR

Fisheries Sampling Evaluation in FLR. A package to interface betwen the SAM stock assessments and FLR, and aid the inclusion of SAM into Management Strategy Evaluation (MSE), including the set up of operating models mimicking SAM.

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2.76 score 2 stars 58 scripts

icesVMS - Link to the ICES Vessel Monitoring System and Logbook Database Web Services

Links to the ICES Vessel Monitoring System (VMS) and logbook database web services <https://data.ices.dk/vms/webservices> to allow users to download summaries and data products.

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2.74 score 2 stars 55 scripts 32 downloads

icesUtils - Functions for processing ICES data and producing ICES shiny applications

A collection of functions useful for processing ICES data and making ICES shiny apps.

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2.70 score

sfdSAR - Functions to calculate Swept area ratio and Surface and subsurface abrasion from VMS data

Functions to calculate Swept area ratio and Surface and subsurface abrasion from VMS data. The data is expected to conform to the ICES WGSFD data call format.

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2.38 score 3 stars 16 scripts

icesSharePoint - Helper functions to interact with the ICES sharepoint

Helper functions to interact with the ICES sharepoint used by the International Council for the Exploration of the Sea (ICES).

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2.35 score 45 scripts

icesASD - Advice and Scenarios Database Web Services

R interface to access the web services of the ICES Advice and Scenarios database <https://asd.ices.dk/AdviceList>.

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1.70 score 8 scripts

icesTAFDB - Transparent Assessment Framework (TAF) Database Web Services

R interface to access the web services of the ICES Transparent Assessment Framework (TAF) Database <http://taf.ices.dk>.

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1.70 score 3 scripts

icesdown - ICES Rmarkdown tools

A collection of rmarkdown and pandoc versions of various ICES templates can be found here.

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1.70 score 1 scripts

rct3 - Functions to Predict Fish Year-Class Strength from Survey Data

Functions to predict fish year-class strength by calibration regression analysis of multiple recruitment index series.

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1.70 score 1 scripts 506 downloads