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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 8 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

FLa4a - A Simple and Robust Statistical Catch at Age Model

A simple and robust statistical Catch at Age model that is specifically designed for stocks with intermediate levels of data quantity and quality.

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6.77 score 13 stars 2 dependents 209 scripts

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

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

FLBEIA - Bio-Economic Impact Assessment of Management Strategies using FLR

A simulation toolbox that describes a fishery system under a Management Strategy Estrategy approach. The objective of the model is to facilitate the Bio-Economic evaluation of Management strategies. It is multistock, multifleet and seasonal. The simulation is divided in 2 main blocks, the Operating Model (OM) and the Management Procedure (MP). In turn, each of these two blocks is divided in 3 components: the biological, the fleets and the covariables on the one hand, and the observation, the assessment and the advice on the other.

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cpp

5.86 score 11 stars 208 scripts

FLife - Methods for Modelling Life History Traits

Many studies have shown the relationships between life history traits for processes such as growth, maturity and natural mortality. Life history has been used to develop priors in stock assesments and to parameterise ecological models. Package has a variety of methods for modelling life history traits and processes.

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5.32 score 2 stars 230 scripts

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

5.18 score 30 stars

FLash - Forecasting and Projection of Fish Stocks

Projecting the future dynamics of fish stocks is an essential part of fisheries science and management advice. The FLash package carries out forecasts of fish stocks (FLStock objects) according to a defined table of targets and limits (fwdControl) and applying and specified stock-recruitment relationship.

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cpp

5.02 score 1 dependents 232 scripts

FLAssess - Generic Classes and Methods for Stock Assessment Models

A generic set of classes for stock assessment models are provided here. Individual assessment packages should extend the basic classes.

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cpp

4.76 score 3 dependents 323 scripts

FLSAM - An Implementation of the State-Space Assessment Model for FLR

This package provides an FLR wrapper to the SAM state-space assessment model.

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4.68 score 5 stars 478 scripts

ss3om - Tools for Conditioning Fisheries Operating Models Using Stock Synthesis 3

Tools for loading Stock Synthesis (SS3) models into FLR. Used in conditioning of Operating Models based on SS3 by considering structural uncertainty in input parameters and assumptions. A grid of SS3 runs can be created and results loaded on objects of various FLR classes.

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fisheriesss3flr

4.53 score 84 scripts

mseviz - Plots and Visualization Tools for Management Strategy Evaluation Results

A set of plots and visualization tools to explore and present the results of Management Strategy Evaluation (MSE) analyses.

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4.19 score 31 scripts

FLXSA - eXtended Survivor Analysis for FLR

Calculates stock numbers and fishing mortality at age from commercial catch data and one or more indices of abundance suing the method in Darby and Flatman (1994) and Shepherd (1999).

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cpp

4.14 score 2 stars 1 dependents 115 scripts

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

FLRef - Reference point computation for advice rules

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3.62 score 3 stars 40 scripts

FLFleet - Classes and Methods for Fleets and Metiers

This package contains classes and methods for modelling of fishing fleets and their activity on multiple fish stocks.

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3.19 score 1 stars 1 dependents 103 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

mpb - Management Procedures

mpb is an R package for running and simulation testing biomass based stock assessment models.

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2.71 score 51 scripts

a4adiags - Additional Diagnostics for FLa4a stock Assessment Models

A series of extra diagnostics for the FLa4a model, including prediction skill through restrospective prediction of model inputs and runs tests. Contains ggplot-based plot funtions of diagnostics outputs.

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2.70 score 8 scripts

AAP - Aarts and Poos Stock Assessment Model that Estimates Bycatch

FLR version of Aarts and Poos stock assessment model.

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2.70 score 8 scripts

msemodules - Modules and Functions for the mse Package

A number of additional modules and auxiliary functions for the 'mse' package are provided here.

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2.65 score 8 scripts

bbm - FLR Implementation of a Two-Stage Stock Assessment Model

The two-stage biomass-based model for the Bay of Biscay anchovy (Ibaibarriaga et al., 2008).

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cpp

1.70 score 5 scripts