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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

MARSS - Multivariate Autoregressive State-Space Modeling

The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models, including partially deterministic models. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Fitting available via Expectation-Maximization (EM), BFGS (using optim), and 'TMB' (using the 'marssTMB' companion package). Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, model selection criteria including bootstrap AICb, confidences intervals via the Hessian approximation or bootstrapping, and all conditional residual types. See the user guide for examples of dynamic factor analysis, dynamic linear models, outlier and shock detection, and multivariate AR-p models. Online workshops (lectures, eBook, and computer labs) at <https://atsa-es.github.io/>.

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multivariate-timeseriesstate-space-modelsstatisticstime-series

10.64 score 54 stars 3 dependents 792 scripts 1.5k downloads

mizer - Dynamic Multi-Species Size Spectrum Modelling

A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.

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ecosystem-modelfish-population-dynamicsfisheriesfisheries-managementmarine-ecosystempopulation-dynamicssimulationsize-structurespecies-interactionstransport-equationcpp

9.70 score 43 stars 310 scripts 468 downloads

FIMS - The Fisheries Integrated Modeling System

The Fisheries Integrated Modeling System is a next-generation framework of stock assessment models, assisting fishery managers with the goal of achieving sustainable fisheries. This system, when completed in a few years, offers the NOAA Fisheries and global fisheries science communities an advanced set of stock assessment models. These tools can be used separately or in combination to incorporate ecosystem and socioeconomic data and models, as well as climate effects and other drivers within the marine environment, into stock assessment models.

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noaa-nsapstock-assessmentcpp

8.95 score 36 stars 74 scripts

Rceattle - Fits the Multispecies Assessment Model (CEATTLE) Using TMB

Implements the CEATTLE model using Template Model Builder ('TMB'; Kristensen et al. 2015), which can be installed following <https://github.com/kaskr/adcomp/wiki/Download>. Structured similar to the original manuscript in terms of modularization. Separate functions estimate retrospective temperature- and size-specific predator rations, prey preference, and weight-at-age. These are then used as inputs to the CEATTLE model to evaluate how predation mortality, recruitment, and survival of three target species change under historical climate conditions and harvest rates.

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8.16 score 12 stars 238 scripts

bayesdfa - Bayesian Dynamic Factor Analysis (DFA) with 'Stan'

Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic factor analysis is a dimension reduction tool for multivariate time series. 'bayesdfa' extends conventional dynamic factor models in several ways. First, extreme events may be estimated in the latent trend by modeling process error with a student-t distribution. Second, alternative constraints (including proportions are allowed). Third, the estimated dynamic factors can be analyzed with hidden Markov models to evaluate support for latent regimes.

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cpp

7.94 score 29 stars 103 scripts 1.0k downloads

Rpath - R implementation of Ecopath with Ecosim

This package implements the core mass balance equations made popular by Ecopath with Ecosim. There are two parts to the package, the static snapshot of energy flow through the system using rpath and dynamic simulations run using the rsim family of functions.

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cpp

7.93 score 41 stars 136 scripts

nmfspalette - A Color Palette for NOAA Fisheries

This is a package that implements a color palette in line with the NOAA Fisheries Branding Guide.

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color-palettenoaanoaa-nsap

7.29 score 36 stars 96 scripts

wham - Woods Hole Assessment Model (WHAM)

The Woods Hole Assessment Model (WHAM) is a general age-structured stock assessment framework that can be configured to estimate assessment models that range in complexity from statistical catch-at-age (SCAA) model with annual recruitments as fixed effects, to state-space, multi-stock, multi-region, age-structured models where many parameters can be treated as time- and age-varying process errors and/or allowing effects of environmental covariates. WHAM is a generalization of code from Miller et al. (2016), Miller and Hyun (2018), and Miller et al. (2018). WHAM also has many similarities of input data sources with ASAP (Legault and Restrepo 1999) and provides functions to generate a WHAM input file from an ASAP3 dat file, although this is not a requirement. Many of the plotting functions for input data, results, and diagnostics have modified from code written by Chris Legault and Liz Brooks.

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fisheries-stock-assessmentstate-spacecpp

6.99 score 43 stars 626 scripts

stockplotr - Tables and Figures for Stock Assessments

Creates exploratory and finished tables and figures for stock assessment documents from U.S. stock assessment model outputs. This packages addresses parts of the stock assessment workflow that interprets outputs of stock assessment models as well as allows the analyst to create report ready tables and figures, reducing the need to create their own and format then when adding into a report. This package is intended to be used in conjuction with 'asar', a partially automated template for writing various stock assessment reports. Throughout development, we will be creating a set of standardized figures and tables for a stock assessment report, developing functions to produce a variety of diagonostic plots, and other helpful materials. The advantage of using this package over others is that it applies to a range of stock assessment model outputs and standardizes them.

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6.55 score 19 stars 8 scripts

adnuts - No-U-Turn MCMC Sampling for 'ADMB' Models

Bayesian inference using the no-U-turn (NUTS) algorithm by Hoffman and Gelman (2014) <https://www.jmlr.org/papers/v15/hoffman14a.html>. Designed for 'AD Model Builder' ('ADMB') models, or when R functions for log-density and log-density gradient are available, such as 'Template Model Builder' models and other special cases. Functionality is similar to 'Stan', and the 'rstan' and 'shinystan' packages are used for diagnostics and inference.

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6.43 score 25 stars 72 scripts 283 downloads

FishSET - Spatial Economics Toolbox for Fisheries

The Spatial Economics Toolbox for Fisheries (FishSET) is a set of tools for organizing data; developing, improving and disseminating modeling best practices.

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economicslocation-choice-modelnwfsc-framcpp

6.41 score 9 stars 12 scripts

SPoRC - A Generalized Stochastic (S) Population (Po) Model Over Regional (R) Components (C)

A generalized spatial population model for stock assessment, written in RTMB.

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6.19 score 7 stars

ghactions4r - Use GitHub Actions Reusable Workflows for R Packages

Provides functions to allow users to set up github action workflows related to R packages.

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github-actionsnoaanoaa-fisheries

5.68 score 16 stars 2 scripts

asar - Build NOAA Stock Assessment Report

Build a full or update stock assessment report for any stock assessment model. Parameterization allows the user to call a template based on their regional science center, species, area, ect.

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latexnoaa-nsapquartostock-assessmentstock-assessment-reports

5.49 score 44 stars 14 scripts

SSMSE - Management Strategy Evaluation (MSE) using Stock Synthesis (SS)

An R package for performing Management Strategy Evaluation (MSE) using Stock Synthesis (SS3). SS3 is used as the Operating Model (OM) and, if the user desires, the Estimation model (EM). SSMSE allows existing SS3 models to be used as the basis for an OM. These OMs are used in the MSE framework provided by SSMSE to evaluate the implications of management actions on a population given uncertainty.

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stock-synthesis

4.89 score 21 stars 61 scripts

bycatch - Fit Bayesian Models to Bycatch Data

Fits models to bycatch data, and can expand to fleet-wide estimates, like in situations when fisheries are observed with less than 100% observer coverage.

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cpp

4.87 score 3 stars 14 scripts

phylosem - Phylogenetic Structural Equation Model

Applies phylogenetic comparative methods (PCM) and phylogenetic trait imputation using structural equation models (SEM), extending methods from Thorson et al. (2023) <doi:10.1111/2041-210X.14076>. This implementation includes a minimal set of features, to allow users to easily read all of the documentation and source code. PCM using SEM includes phylogenetic linear models and structural equation models as nested submodels, but also allows imputation of missing values. Features and comparison with other packages are described in Thorson and van der Bijl (2023) <doi:10.1111/jeb.14234>.

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cpp

4.56 score 1 stars 18 scripts 243 downloads

AgeingError - Estimating ageing error with 'TMB' from double reads

Implements Generalized Linear Mixed Effect Models (GLMMs) using TMB to estimate ageing error from double reads of otoliths. The original analysis (Punt et al. 2008; <doi:10.1139/F08-111>) was written in ADMB and focused on estimating imprecision and bias. The newer version of the software allows for random effects using TMB.

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cpp

4.52 score 11 stars 9 scripts

NWCTrends - Standardized Trend Metrics for Salmonid Populations

This is runs the standardized trends metrics used in the 2016 and 2020 5-year NWFSC Viability Reports for listed PNW salmonids. To run, type library(NWCTrends) and then NWCTrends_report().

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marssnoaaprotected-speciessalmontime-series

3.48 score 2 stars 7 scripts

LHsampling - Functions For Simulating Fish Populations And Estimating Life History Parameters

An individual-based model (IBM) incorporating within-population variability in von Bertalanffy growth, size-dependent natural mortality, and a size-selective fishery to simulate an exploited fish population and catch (harvest). A bootstrap algorithm allows the user to investigate various sampling approaches including sampling strategy (proportional or fixed otolith sampling, POS or FOS, respectively), sample size, supplementation with fishery-independent sampling, and assumptions regarding von Bertalanffy t0 and the relationship between variance of length at age and age. A function to produce plots of the bootstrap sampling results is also provided.

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3.18 score 3 stars 6 scripts

eSDM - Ensemble Tool for Predictions from Species Distribution Models

A tool which allows users to create and evaluate ensembles of species distribution model (SDM) predictions. Functionality is offered through R functions or a GUI (R Shiny app). This tool can assist users in identifying spatial uncertainties and making informed conservation and management decisions. The package is further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.

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3.10 score 25 scripts 271 downloads

ghBackup - An R Package that Backs Up your GitHub Repositories

Provide functions to allow users to back up repositories in organizations.

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3.00 score 4 scripts

rCAX - Coordinated Assessments REST API R Client

This package is an R client for the StreamNet Coordinated Assessments HLI REST API.

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noaarest-apisalmon

2.85 score 5 stars 14 scripts

ageproR - R package interface for AGEPRO (Age Structured Projection Model) data

Object-oriented data structures based on the input file format defined in the Age Structured Projection Model Reference Manual. Includes support modules for AGEPRO input file support, and experimental JSON input file format.

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2.60 score 1 stars 2 scripts

ObsCovgTools - Evaluate Fishery Observer Coverage for Bycatch Estimation

Tools for evaluating observer coverage with respect to documenting and estimating rare bycatch, including (1) probabilities of observing a bycatch event and of one occurring in total effort, (2) upper confidence limit for bycatch given none was observed, and (3) bycatch estimation CV (coefficient of variation).

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2.18 score 3 stars 1 scripts

FishEconProdOutput - Price Method Fisheries Economics Total Factor Productivity Outputs

Here we provide methodology guidelines on how to calculate fishery productivity measurement at the individual fishery and aggregate sector levels. Attention is given to the constructions of output and total factor productivity based on available data and a bottom-up approach. Given that there is no nation-wide standard cost survey, we recommend starting with measuring TFP at the fishery level based on a translog gross output production possibility frontier using index number techniques. Special attention is given to measuring quality-adjusted physical capital inputs in the bottom-up approach.

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departmenteconomicsfisheriesnational-oceanicnoaanoaa-fisheries-officeproductivityopenjdk

1.70 score