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 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.

Last updated 15 days ago

fisheriesfisheries-stock-assessmentstock-synthesis

11.36 score 39 stars 2 dependents 1.0k scripts 440 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://flr-project.org/>.

Last updated 10 days ago

fisheriesflrfisheries-modelling

8.75 score 16 stars 23 dependents 948 scripts 49 downloads

stockassessment - State-Space Assessment Model

Fitting SAM...

Last updated 6 days ago

stockassessmentcpp

7.72 score 49 stars 2 dependents 318 scripts

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.

Last updated 17 hours ago

visualizationggplot2fisheriesflr

7.69 score 4 stars 12 dependents 458 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.

Last updated 2 months ago

simulationmsefisheriesflra4a

6.80 score 4 stars 3 dependents 146 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.

Last updated 2 months ago

reference pointsfisheriesflrcpp

6.58 score 2 stars 4 dependents 350 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.

Last updated 14 days ago

forecastfisheriesflrcpp

6.56 score 2 stars 6 dependents 254 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.

Last updated 23 days ago

6.49 score 12 stars 2 dependents 177 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.

Last updated 4 days ago

cpp

5.94 score 11 stars 159 scripts

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.

Last updated 2 months ago

cpp

4.92 score 1 dependents 186 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.

Last updated 2 months ago

4.81 score 4 stars 406 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.

Last updated 2 months ago

cpp

4.77 score 3 dependents 324 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).

Last updated 2 months ago

cpp

4.36 score 2 stars 1 dependents 95 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.

Last updated 2 months ago

fisheriesss3flr

3.82 score 44 scripts

FLSRTMB - FLSR in TMB

Estimates FLR spawner recruitment relationships in TMB

Last updated 2 months ago

stock-recruitfisheriesflrtmbadcpp

3.67 score 1 dependents 26 scripts

FLRef - Reference point computation for advice rules

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Last updated 6 days ago

3.36 score 3 stars 11 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.

Last updated 2 years ago

3.11 score 1 stars 1 dependents 86 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.

Last updated 2 months ago

fisheriesflr

3.02 score 7 dependents 8 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.

Last updated 7 months ago

3.00 score 10 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.

Last updated 3 years ago

2.71 score 2 stars 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.

Last updated 1 years ago

2.70 score 7 scripts

AAP - Aarts and Poos Stock Assessment Model that Estimates Bycatch

FLR version of Aarts and Poos stock assessment model.

Last updated 1 years ago

2.70 score 6 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).

Last updated 2 years ago

cpp

2.70 score 5 scripts