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

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

jjmR - Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model

Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model.

afscdata - An R Package for Extraction of AFSC Fishery Data

This package provides a folder structure and SQL queries for accessing the AKFIN and AFSC databases in support of fishery stock assessments. Additionally, archived data are held/provided to maintain consistency across assessments/assessment authors.

rema - A generalized framework to fit the random effects (RE) model, a state-space random walk model developed at the Alaska Fisheries Science Center (AFSC) for apportionment and biomass estimation of groundfish and crab stocks.

This package provides a generalized framework to fit the random effects (RE) model, a state-space random walk model developed at the Alaska Fisheries Science Center (AFSC) for smoothing survey biomass estimates and apportioning catch among management areas. REMA is a multivariate extension of the original single-survey, single-strata RE model that allows the use of multiple strata within a survey and an additional survey (e.g. CPUE or relative population numbers) to inform the biomass trend (Hulson et al. 2021). If multi-survey mode is turned off, REMA runs the same as the univariate (RE) and multivariate (i.e. multiple area or depth strata; REM) versions of the model. REMA was developed in Template Model Builder (TMB; Kristensen et al. 2016).

FLjjm - Running the JJM Stock Assessment Model Inside the MSE FLR System

Runs the JJM stock assessment model for Chilean Jack Mackerel inside the MSE system of FLR's mse package.

ebswp - Facilitates Model Running for EBS Pollock

Facilitates model running for EBS Pollock.

planteam - Making Plan Team Smoother

Create planteam summaries, catch reports, and spec tables

afscISS - Retrieve composition data ISS

Retrieve bootstrap estimates of age/length/conditional age-at-length input sample size produced by the surveyISS package.

pkgdownTemplate - pkgdown Template Package

This is a template package for a NMFS branded R package with a pkgdown website.

sa4all - Write Stock Assessments for general purposes

Create files and the structure necessary to facilitate rapid and reproducible creation of stock assessment documents from model output generated by Stock Synthesis (SS). The included components and structure are specific to requests from the Pacific Fisheries Management Council for US West Coast groundfish.

inseasonDashboard - In-Season Fishery Monitoring Tools

Tools for accessing AFSC and AKFIN databases and producing standardized in-season fishery summaries and diagnostics.

WtAgeRe - Fish Body Mass at Age Estimation

A random effects model for estimating variance in weight-at-age, with utilities to read ADMB outputs and plot weight-at-age anomalies.

growthbreaks - Spatio-temporal Growth Anomaly Detection

Implements the GAM-based breakpoint detection method for length-at-age observations as described Kapur et. al. 2019.

catchfunction - BSAI catch function

contains function which calculates catch in BS, and one that returns TAC estimate on BS/BSAI level as appropriate.

funplots - Exploratory plots of Alaskan survey and fisheries data in support of stock assessment

Pulls in survey, observer and catch data from the Eastern Bering Sea, Northern Bering Sea, Aleutian Islands, and Gulf of Alaska and automates creation of plots for each groundfish species to understand time-varying, seasonal, and spatial aspects of these fish populations and fisheries. This package was created in support of Alaska stock assessment science to inform model specification and interpretation.

nwfscAgeingError - Source Code for Punt et al. (2008): Ageing Error and Imprecision

Source code and examples for how to use double-read data to estimate ageing imprecision and bias from fishery otoliths. The code was developed for Punt et al. (2008) and updated in 2022.

VRData - This is a data package for the spawner and fraction wild data used in the NWFSC PNW Salmonid Viability Reports.

fmR - What the Package Does (One Line, Title Case)

What the package does (one paragraph).

SARA - This is a package for the AFSC Groundfish stock assessment results