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 3.30.22, from October 2023). Support for 3.24 models is only through the core functions for reading output and plotting.

Last updated 2 days ago

fisheriesfisheries-stock-assessmentstock-synthesis

11.32 score 38 stars 2 packages 1.0k scripts 532 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.

Last updated 15 days ago

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

9.41 score 38 stars 226 scripts 570 downloads

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.

Last updated 1 months ago

8.56 score 28 stars 99 scripts 1.0k 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/>.

Last updated 1 years ago

7.61 score 3 packages 604 scripts 897 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.

Last updated 6 months ago

7.19 score 29 stars 111 scripts

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.

Last updated 4 months ago

7.11 score 16 stars 20 scripts

glmmfields - Generalized Linear Mixed Models with Robust Random Fields for Spatiotemporal Modeling

Implements Bayesian spatial and spatiotemporal models that optionally allow for extreme spatial deviations through time. 'glmmfields' uses a predictive process approach with random fields implemented through a multivariate-t distribution instead of the usual multivariate normal. Sampling is conducted with 'Stan'. References: Anderson and Ward (2019) <doi:10.1002/ecy.2403>.

Last updated 1 years ago

ecologyextremesspatial-analysisspatiotemporal

6.73 score 50 stars 54 scripts 696 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.

Last updated 7 days ago

economicslocation-choice-modelnwfsc-fram

6.63 score 4 stars 12 scripts

wham - Woods Hole Assessment Model (WHAM)

The Woods Hole Assessment Model (WHAM) is a state-space age-structured stock assessment model that can include environmental effects on population processes. WHAM can be configured to estimate a range of assessment models: a traditional statistical catch-at-age (SCAA) model with recruitments as fixed effects, SCAA with recruitments as random effects, or a "full state-space" model with abundance at all ages treated as random effects. WHAM is a generalization of the R and TMB 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. Many of the plotting functions for input data, results, and diagnostics are modified from ASAP code written by Chris Legault and Liz Brooks.

Last updated 4 months ago

fisheries-stock-assessmentstate-space

6.50 score 32 stars 354 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.

Last updated 10 months ago

6.29 score 23 stars 57 scripts 299 downloads

ghactions4r - Use GitHub Actions Reusable Workflows for R Packages

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

Last updated 6 days ago

github-actionsnoaanoaa-fisheries

5.76 score 12 stars 2 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>.

Last updated 12 days ago

5.23 score 1 stars 14 scripts 225 downloads

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

An R package for performing Management Strategy Evaluation (MSE) using Stock Synthesis (SS). SS is used as the Operating Model (OM) and, if the user desires, the Estimation model (EM). SSMSE allows existing SS 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.

Last updated 6 months ago

stock-synthesis

5.46 score 18 stars 53 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.

Last updated 4 months ago

color-palettenoaa

5.09 score 29 stars 53 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.

Last updated 5 months ago

4.08 score 3 stars 4 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>.

Last updated 4 months ago

3.91 score 23 scripts 376 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`.

Last updated 2 months ago

3.73 score 9 stars 2 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.

Last updated 10 months ago

3.18 score 3 stars 6 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().

Last updated 1 years ago

marssnoaaprotected-speciessalmontime-series

3.18 score 1 stars

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).

Last updated 4 months ago

2.48 score 3 stars 1 scripts

ghBackup - An R package that backs up your GitHub repositories

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

Last updated 2 years ago

1.70 score 4 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.

Last updated 3 years ago

departmenteconomicsfisheriesnational-oceanicnoaanoaa-fisheries-officeproductivity

1.70 score