tier4tools

Tier 4 Spawning Potential Ratio (SPR) reference points in Alaska groundfish stock assessments

tier4tools is an R package developed to support stock assessment scientists develop North Pacific Fishery Management Council (NPFMC) Tier 4 alternatives for Alaskan groundfish stocks. The package provides a transparent, reproducible workflow for computing SPR-based reference points when full age-structured models are not available or not appropriate.

This package provides:

• consistent implementation of SPR analyses for single-species and multispecies stocks,

• report-ready visualizations and output,

• diagnostic tools for understanding sources of uncertainty in SPR-based reference points.

Installation and Development

tier4tools is under active development and is not yet on CRAN. You can install the development version from GitHub:

devtools::install_github("noaa-afsc/tier4tools", build_vignettes = TRUE)

Issues, suggestions, and contributions are welcome via GitHub.

Basic Workflow

A typical Tier 4 analysis using tier4tools follows four main steps:

1. Define biological and fishery inputs using spr_input(). Visualize and validate inputs using plot_spr_inputs().

2. Compute per-recruit objects and SPR-based reference points (e.g., F40%, F35%) using run_spr(). Visualize results with plot_spr_curves().

3. Show age decomposition and plus group diagnostics for spawning biomass per recruit (SBPR) contributions, removals, and survivorship using plot_spr_decomp().

4. Run structured sensitivity analyses on key SPR input parameters (e.g., maturity, fishery selectivity, natural mortality) using spr_sensitivity(). Visualize results using plot_sensitivity_heatmap(). For multispecies applications, sensitivity analyses for recruitment allocation by species are also available. These results can be visualized using plot_recprop_sensitivity().

Vignettes

Detailed examples are available in the package vignettes, including:

• single-species Tier 4 workflows,

• multispecies per-recruit analyses,

• interpretation of age decomposition plots and sensitivity results

browseVignettes("tier4tools")